data-raw/lm/processMCFO.R
In jefferislab/lhns: Skeleton data for neurons associated with the lateral horn of Drosophila melanogaster
##################################
# Read and process MCFO skeletons #
#################################
# Prepare data on Mike's splits
if(!exists("most.lhns")){
stop("Please run processLHNs.R!")
}else if(!exists("most.lhins")){
stop("Please run processLHNinputs.R!")
}
most.lhns.old = most.lhns
most.lhins.old = most.lhins
# Use olf Frechter et al. names for this file
if(!is.null(most.lhns.old[,"frechter.cell.type"])){
most.lhns.old[,"cell.type"] = most.lhns.old[,"frechter.cell.type"]
}
if(!is.null(most.lhins.old[,"frechter.cell.type"])){
most.lhins.old[,"cell.type"] = most.lhins.old[,"frechter.cell.type"]
}
# # Read MCFO neurons
# mcfo = read.neurons("/Users/abates/ImageData/MCFO/lastish_stacks/skels4")
# mcfo = nlapply(mcfo,nat::resample, stepsize = 1)
#
# # Fix skeletons (fix a few issues with Amira skeletons, like loops and star-burst node connectivity)
# nl = nat::neuronlist()
# for(mn in mcfo){
# file = names(mcfo)[length(nl)+1]
# message(length(nl)+1)
# x = nat::xyzmatrix(mn)
# k = 10
# swc = data.frame(PointNo = 1:nrow(x),Label = 0,x,W = -2, Parent = -1, tree = NA) # Create SWC data.frame
# nears = nabor::knn(data = x, query = x, k = k) # Find the closest k nodes
# all.dists = nabor::knn(data = x, query = x, k = nrow(x)) # Find the closest k nodes
# skel = 1 # We will grow our tree from, as start, the root for the first skeleton as the first point
# used = c()
# d = 0.1 #mean(nears[[2]][,-1]) # Start with the smallest connection distance, then grow the connection distance to its maximum. dd is the lower bound.
# distance.steps = 0.1
# connection.distance = 100 #max(nears[[2]][,c(2,3)]) # Max distance by which nodes can be connected
# parents = nears[[1]][,-1][which.min(all.dists[[2]][,-1])] # Start with a faux 'root'
# used = c()
# print(d)
# while(sum(is.na(swc$tree))>0) {
# if(all(parents%in%used)){ # If we run out of nodes in the connection range
# skel = skel + 1; leaves = c()
# dists = nears[[2]][-1*used,-1]
# indices = nears[[1]][-1*used,-1]
# parents = indices[which.min(dists)]
# parents = subset(swc,is.na(tree))$PointNo[[1]]
# }
# search = nears[[1]]; search[!nears[[2]]<=d] = NA # Get the closest matches in space to each non-zero point in the image stack
# used = c(used,parents) # Parent nodes cannot be assigned to matches already within the tree
# children = search[parents,]# Find the right match row
# children = unique(children[!is.na(children)]) # Get children, i.e. candidate child nodes, within the connection distance
# children = children[!children%in%used] # Remove the nodes we have already added to our skeleton
# swc[unique(c(parents,children)),"tree"] = skel # So now we'll assign them to a skeleton
# if(length(children[!is.na(children)])>0){ # If there are children
# if(length(children)>1){
# closest.parents = apply(search[children,],1, function(x) x[x%in%parents][1])
# if(sum(is.na(closest.parents))>0){ # The the closest parent is not within the top k matches, look the other way
# lost = children[is.na(closest.parents)]
# closest.parents[is.na(closest.parents)] = sapply(lost,function(x) rep(parents,k)[which.max(search[parents,]==x)[1]])
# }
# }else{
# closest.parents = search[children,][search[children,]%in%parents][1]
# if(sum(is.na(closest.parents))>0){ # The the closest parent is not within the top k matches, look the other way
# closest.parents = rep(parents,k)[which.max(search[parents,]==children)][1]
# }
# }
# swc[children,"Parent"] = closest.parents # Assign to the closest parent
# parents = children # Now grow tree from the old children
# }
# }
# # Now we have created a bunch of skeletons at the minimal connection distance, d.
# # We need to grow our search aread to d.max and so merge these different skeletons
# dd = d # Minimal
# d = d + distance.steps # Maximal
# while(d<=connection.distance){
# # Get the indices within the search distance
# print(d)
# search = nears[[1]]
# search[!nears[[2]]<=d] = NA
# search[!nears[[2]]>dd] = NA
# # Get the distances
# dists = nears[[2]]
# m = reshape2::melt(dists)
# m = subset(m,value<=d)
# m = subset(m,value>dd)
# # Order indices to grow by shortest distance to next node
# m = m[order(m$value),]
# for(parent in m$Var1){
# t = swc[parent,"tree"]
# used = subset(swc,tree==t)$PointNo
# children = search[parent,]# Find the right match row
# children = unique(children[!is.na(children)]) # Get children, i.e. candidate child nodes, within the connection distance
# children = children[!children%in%used] # Remove the nodes we have already added to our tree
# children = children[!duplicated(swc[children,"tree"])] # Children must be in different trees from one another
# if(length(children)>0){
# for(child in children){ # Now combine the trees
# child.tree = swc[as.character(child),"tree"]
# n = subset(swc,tree==child.tree)
# if(nrow(n)>1){ # Connect another tree
# n = nat::as.neuron(nat::as.ngraph(n), origin = child)$d
# # el = n[n$Parent != -1, c("Parent", "PointNo")]
# # el = el[el$Parent%in%n$PointNo,]
# # n = ngraph(data.matrix(el), n$PointNo, directed = TRUE, xyz = xyzmatrix(n), diam = n$W)
# # n = nat::as.neuron(n)$d
# n$tree = t
# n[n$PointNo==child,"Parent"] = parent
# swc[n$PointNo,] = n
# }else if (nrow(n)==1){ # Connect isolated node
# n$tree = t
# swc[swc$PointNo==child,"Parent"] = parent
# swc[as.character(n$PointNo),"tree"] = t
# }
# }
# }
# }
# # Increase the search distance
# dd = d # New min
# d = d + distance.steps # New max
# }
# isolated = sapply(swc$PointNo,function(x) (!x%in%swc$Parent)&(swc[x,"Parent"]==-1))
# swc = swc[!isolated,] # Remove isolated nodes
# swc = swc[!is.na(swc$PointNo),]
# nn = nat::as.neuron(swc)
# nams = c(names(nl),file)
# nl = c(nl,nat::as.neuronlist(nn))
# names(nl) = nams
# }
# attr(nl,"df") = data.frame(file=names(mcfo))
# nl = nlapply(nl,nat::resample, stepsize = 1)
# names(nl) = as.character(nl[,"file"])
#
# # Fit soma - interactive
# nl = catnat::correctsoma(nl)
# names(nl) = as.character(nl[,"file"])
#
# # Flip neurons - interactive
# nopen3d();plot3d(nl,soma=T);plot3d(JFRC2013)
# left.side.neurons = nat::find.soma(db=nl)
# nl[left.side.neurons] = mirror_brain(nl[left.side.neurons],brain = JFRC2013)
#
#
# # Transform to FCWB space
# mcfo4 = nat::nlapply(nl,nat.templatebrains::xform_brain,sample = nat.flybrains::JFRC2013,reference= nat.flybrains::FCWB,OmitFailures = T) # any lost?
# # # save
# # save(mcfo,file = "data-raw/dolan_mcfo.rda")
#################################
# Meta-data for the MCFO object #
#################################
# Load data
load("data-raw/dolan_mcfo.rda")
for(i in 1:length(mcfo)){
mcfo[[i]]$d$Label = 0
}
# Detect and remove duplicated skeletons
# Get the imade code to line mapping
dcs = read.csv("data-raw/csv/dolan_cells.csv")
dcs$ImageCode = NULL
dcs = aggregate(No_Cells ~ LineCode + old.cell.type, dcs, function(x) paste0(round(mean(x)),ifelse(!is.na(sd(x)),paste0("±",round(sd(x))),"")))
colnames(dcs) = c("LineCode","old.cell.type","no.cells")
nts = read.csv("data-raw/csv/NT_annotation_from_Mike.csv")
stainings = merge(dcs,nts,all.x=TRUE,all.y=TRUE)
codes = read.csv("data-raw/csv/FlycoreCodes.csv")
s = as.character(codes[,"Genotype"])
# Work out metadata
d = read.csv("data-raw/csv/SplitGAL4annotate.csv",header = TRUE)
colnames(d) = c("linecode","imagecode","AD","DBD","old.cell.type","num.lh.clusters","Ideal","Behaviour","MCFO","Polarity","Stablestock","VNC","ImagePath")
d$imagecode = NULL
d = d[!duplicated(d$linecode),]
rownames(d) = d$linecode
m = c();lines = c(); nams = c()
for(nam in names(mcfo)){
n = gsub("^4a_","",nam)
n = gsub("^cell1_","",n)
n = gsub("*-.*","",n)
n = gsub(".*_","",n)
if(n=="01"){
n="37G11"
}
mch = match(n,s)
lines = c(lines,ifelse(is.na(mch),n,as.character(codes[mch,"LineCode"])))
m = c(m,mch)
nams = c(nams, n)
}
#mf = data.frame(linecode = codes[m,"LineCode"])
mf = data.frame(linecode = as.character(lines))
mf$genotype = codes[m,"Genotype"]
mf = cbind(mf,d[as.character(mf$linecode),])
mf[,c("pnt","anatomy.group","cell.type","type")] = "notLHproper"
mf$match = NA
mf$skeleton.type = "MCFO"
mf$file = rownames(mf) = names(mcfo)
mf[] = lapply(mf, as.character)
mf = mf[,!colnames(mf)%in%c("linecode.1","ImagePath")]
# # NBlast
# mcfo.dps = dotprops(mcfo,resample=1)
# result1 = nblast(mcfo.dps, c(lhns::most.lhns.dps,lhns::most.lhins.dps))
# result2 = nblast(c(lhns::most.lhns.dps,lhns::most.lhins.dps), mcfo.dps)
# result = (result1 + t(result2))/2
# most.lh = c(lhns::most.lhns,lhns::most.lhins)
# for(c in 1:ncol(result)){
# clear3d()
# plot3d(FCWB)
# message(paste0(c,"/",ncol(result)))
# message(names(mcfo[c]))
# plot3d(mcfo[c],col = "black",lwd=3,soma=T)
# n = nlscan(most.lh[names(sort(result[,c],decreasing = TRUE))],col="red",lwd=2,soma=T)
# }
##############################
# Assignments to LHN library #
##############################
# L1477; 4A
mf[c("JRC_SS22624-20160701_21_D6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22624-20160701_21_D7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22624-20160701_21_D8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf[c("JRC_SS22624-20160701_21_D6-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Cha-F-100412"
mf[c("JRC_SS22624-20160701_21_D7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "VGlut-F-500253"
mf[c("JRC_SS22624-20160701_21_D8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "VGlut-F-600752"
# L1721; 16C
mf[c("JRC_SS22713-20160624_20_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22713-20160624_20_C6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22713-20160624_20_C7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "16C"
mf[c("JRC_SS22713-20160624_20_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22713-20160624_20_C6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22713-20160624_20_C7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "Cha-F-400246"
# L2033; 145
mf[c("JRC_SS23107-20160701_22_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23107-20160701_22_C5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "145"
mf[c("JRC_SS23107-20160701_22_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23107-20160701_22_C5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Gad1-F-600202"
# L2098; 1A
mf[c("JRC_SS23129-20160805_24_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23129-20160805_24_C4-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$old.cell.type = "1A2"
mf[c("JRC_SS23129-20160805_24_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23129-20160805_24_C4-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$match = "Gad1-F-200366"
# L2233; 4E
mf[c("JRC_SS23187-20160805_23_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F7-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$old.cell.type = "4E"
mf[c("JRC_SS23187-20160805_23_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F7-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$match = "Cha-F-200398"
# L1959; 29G
mf[c("JRC_SS23354-20160909_25_H1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "29G"
mf[c("JRC_SS23354-20160909_25_H1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "VGlut-F-500445"
# L1847; 54C
mf[c("JRC_SS23805-20160902_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54C"
mf[c("JRC_SS23805-20160902_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-800092"
# L1900; 85
mf[c("JRC_SS23817-20170623_24_B1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "85"
mf[c("JRC_SS23817-20170623_24_B1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "MB-C1"
# L452; 27C
mf[c("JRC_SS22532-20160928_31_C1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "27C"
mf[c("JRC_SS22532-20160928_31_C1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-500140"
# MB036B;
mf[c("GMR_MB036B-20151217_22_C2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "3C"
mf[c("GMR_MB036B-20151217_22_C2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Cha-F-800045"
# MB072C;
mf[c("GMR_MB072C-20151105_25_E2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "120"
mf[c("GMR_MB072C-20151105_25_E2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "fru-M-000360"
# fru-M-000179
# SS01371;
mf[c("GMR_SS01371-20151105_25_C7-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS01371-20151105_25_D6-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "16A"
mf[c("GMR_SS01371-20151105_25_C7-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS01371-20151105_25_D6-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "AD1d1"
# L163;
mf[c("JRC_SS03224-20150828_23_B5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03224-20151002_21_C3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "3D"
mf[c("JRC_SS03224-20150828_23_B5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03224-20151002_21_C3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Cha-F-500250"
# L528;
mf[c("JRC_SS03237-20151015_19_D2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "141"
mf[c("JRC_SS03237-20151015_19_D2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-300290"
# L849;
mf[c("JRC_SS04948-20151217_26_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04948-20151217_26_B5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "3F"
mf[c("JRC_SS04948-20151217_26_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04948-20151217_26_B5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Cha-F-300342"
# L19;
mf[c("JRC_SS06600-20151002_20_B3-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "8A"
mf[c("JRC_SS06600-20151002_20_B3-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Cha-F-000533"
# L20;
mf[c("JRC_SS15113-20151009_19_C4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "8A"
mf[c("JRC_SS15113-20151009_19_C4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Cha-F-000533"
# L304;
mf[c("JRC_SS15279-20170303_21_B4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "8A"
mf[c("JRC_SS15279-20170303_21_B4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "Cha-F-000533"
# L85;
mf[c("JRC_SS15297-20151002_20_C2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15297-20151002_20_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15297-20151002_20_C8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15297-20161028_17_A1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15297-20161028_17_A1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "51B"
mf[c("JRC_SS15297-20151002_20_C2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15297-20151002_20_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15297-20151002_20_C8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15297-20161028_17_A1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Cha-F-000086"
mf[c("JRC_SS15297-20161028_17_A1-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "Cha-F-000086" # Almost, but not quite...
# L1397;
mf[c("JRC_SS16027-20151022_19_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16027-20151022_19_E1-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS16027-20151022_19_E5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "29G"
mf[c("JRC_SS16027-20151022_19_E1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "VGlut-F-500445"
mf[c("JRC_SS16027-20151022_19_E1-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$match ="VGlut-F-900028"
mf[c("JRC_SS16027-20151022_19_E5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "VGlut-F-900028"
# L787;
mf[c("JRC_SS16564-20160311_23_D7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16564-20160311_23_D7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16564-20160311_23_D8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "1A"
mf[c("JRC_SS16564-20160311_23_D7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "Gad1-F-200366" # OR Gad1-F-200155
mf[c("JRC_SS16564-20160311_23_D7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "AV4f1"
mf[c("JRC_SS16564-20160311_23_D8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-200366" # OR Gad1-F-200155
# L494;
mf[c("JRC_SS16659-20170303_25_B2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16659-20170303_25_B5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "16A2"
mf[c("JRC_SS16659-20170303_25_B2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16659-20170303_25_B5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Gad1-F-500014"
# L1554;
mf[c("JRC_SS22656-20160701_22_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22656-20160701_22_F8-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "3C"
mf[c("JRC_SS22656-20160701_22_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22656-20160701_22_F8-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Cha-F-800045"
# L1614;
mf[c("JRC_SS22675-20160624_20_A1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "16F"
mf[c("JRC_SS22675-20160624_20_A1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "fru-F-300009"
# L1900;
mf[c("JRC_SS23817-20170623_24_B4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "85"
mf[c("JRC_SS23817-20170623_24_B4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "MB-C1"
# L1955;
mf[c("JRC_SS23824-20160909_26_A4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54C"
mf[c("JRC_SS23824-20160909_26_A4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-800092"
# L2087;
mf[c( "JRC_SS24177-20160909_26_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24177-20160909_26_F4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24177-20160909_26_F4-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS24177-20160909_26_F5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "84"
mf[c( "JRC_SS24177-20160909_26_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24177-20160909_26_F4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24177-20160909_26_F4-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS24177-20160909_26_F5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-300218"
# L2088;
mf[c("JRC_SS24659-20161104_18_A2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24659-20161104_18_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24659-20161104_18_A2-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "84"
mf[c("JRC_SS24659-20161104_18_A2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24659-20161104_18_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24659-20161104_18_A2-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$match = "Gad1-F-300218"
# L2392;
mf[c("JRC_SS24820-20161007_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt3.SptGraph.swc"),]$old.cell.type = "76B"
mf[c("JRC_SS24820-20161007_29_F1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt3.SptGraph.swc"),]$match = "VGlut-F-400240"
# L2316;
mf[c("JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "76B"
mf[c("JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$match = "VGlut-F-700280"
# L475;
mf[c( "JRC_SS30939-20161007_30_B7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS30939-20161007_30_B7-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$old.cell.type = "16A2"
mf[c( "JRC_SS30939-20161007_30_B7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS30939-20161007_30_B7-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$match = "Gad1-F-300262"
# L1668; 70A
mf[c("JRC_SS03791-20151105_24_E2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03791-20151105_24_E2-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS03791-20151105_24_E3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03791-20151105_24_E6-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "70A"
mf[c("JRC_SS03791-20151105_24_E2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03791-20151105_24_E2-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS03791-20151105_24_E3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03791-20151105_24_E6-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "WED-PN3"
# L1518; 70A
mf[c("JRC_SS03801-20151125_19_B2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70A"
mf[c("JRC_SS03801-20151125_19_B2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "WED-PN3"
# L1129; 7A
mf[c("JRC_SS04950-20170303_21_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04950-20170303_21_A2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04950-20170303_21_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04950-20170303_21_A5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04950-20170303_21_A6-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "7A"
mf["JRC_SS04950-20170303_21_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-600143"
mf["JRC_SS04950-20170303_21_A2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-600143"
mf["JRC_SS04950-20170303_21_A2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-800078"
mf["JRC_SS04950-20170303_21_A5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-800082"
mf["JRC_SS04950-20170303_21_A6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-600143"
# L1129; 70C
mf[c("JRC_SS04961-20151217_26_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E8-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "70C"
mf["JRC_SS04961-20151217_26_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E8-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match = "VGlut-F-500810"
# L1337; 70B
mf[c("JRC_SS04962-20151125_23_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70B"
mf[c("JRC_SS04962-20151125_23_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "WED-PN5"
# L452; 70A
mf[c("JRC_SS15280-20151015_19_G1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15280-20151015_19_G4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15280-20151015_19_G4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70A"
mf[c("JRC_SS15280-20151015_19_G1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15280-20151015_19_G4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15280-20151015_19_G4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "WED-PN3"
# L788; 1D
mf[c("JRC_SS16038-20151125_23_G1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16038-20151125_23_G1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16038-20151125_23_G1-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "1D"
mf["JRC_SS16038-20151125_23_G1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "fru-F-700136"
mf["JRC_SS16038-20151125_23_G1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "fru-F-700136"
mf["JRC_SS16038-20151125_23_G1-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match = "fru-F-700136"
# L112; 7OC
mf[c("JRC_SS16337-20151125_20_D4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16337-20151125_20_D5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16337-20151125_20_D7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16337-20151125_20_D8-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "7OC"
mf["JRC_SS16337-20151125_20_D4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS16337-20151125_20_D5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS16337-20151125_20_D7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS16337-20151125_20_D8-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
# L1117; 7A
mf[c("JRC_SS16351-20160819_23_C4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "7A"
mf["JRC_SS16351-20160819_23_C4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-500832" # Not in line
mf["JRC_SS16351-20160819_23_C4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-600143"
mf["JRC_SS16351-20160819_23_C6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-200185"
# L271; 7A
mf[c("JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS21811-20161007_29_B7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "7A"
mf["JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-200185"
mf["JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match ="Cha-F-200185"
mf["JRC_SS21811-20161007_29_B7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-800082"
mf["JRC_SS21811-20161007_29_B8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-200185"
# L1524; 70D;
mf[c("JRC_SS22640-20161007_30_D3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22640-20161007_30_D3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22640-20161007_30_D5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22640-20161007_30_D8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "70D"
mf["JRC_SS22640-20161007_30_D3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000514"
mf["JRC_SS22640-20161007_30_D3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000514"
mf["JRC_SS22640-20161007_30_D5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000514"
mf["JRC_SS22640-20161007_30_D8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000514"
# L770 ; 70C
mf[c("JRC_SS22763-20170324_30_A3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22763-20170324_30_A3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70C"
mf["JRC_SS22763-20170324_30_A3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-500810"
mf["JRC_SS22763-20170324_30_A3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500810"
# L772; 70C
mf[c("JRC_SS22764-20170428_25_C3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22764-20170428_25_C8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "70C"
mf["JRC_SS22764-20170428_25_C3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500810"
mf["JRC_SS22764-20170428_25_C8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500810"
# L2001; 147
mf[c("JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt3.SptGraph.swc",
"JRC_SS23097-20160624_20_F3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F8-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "147"
mf["JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt3.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F8-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match = "Gad1-F-200237"
# L2002; 147
mf[c("JRC_SS23098-20160805_24_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23098-20160805_24_B6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "147"
mf["JRC_SS23098-20160805_24_B4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23098-20160805_24_B6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
# L2185; 29B
mf[c("JRC_SS23170-20160805_23_D3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23170-20160805_23_D6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "29B"
mf[c("JRC_SS23170-20160805_23_D3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23170-20160805_23_D6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "PV6a3"
# 70A: L1949
mf[c("JRC_SS23376-20170324_28_D3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23376-20170324_28_D5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23376-20170324_28_D5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70A"
mf[c("JRC_SS23376-20170324_28_D3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23376-20170324_28_D5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23376-20170324_28_D5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "WED-PN3"
# L2193; 29B
mf[c("JRC_SS24679-20161104_18_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B5-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS24679-20161104_18_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B6-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "29B"
mf[c("JRC_SS24679-20161104_18_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B5-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS24679-20161104_18_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B6-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$match = "PV6a3"
# NP6099; TypeII
mf[c("VZJ_K_39601-20180315_20_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"VZJ_K_39601-20180315_20_B1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"VZJ_K_39601-20180315_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"VZJ_K_39601-20180315_20_B2-Aligned63xScale_c0.Smt.SptGraph.swc",
"VZJ_K_39601-20180315_20_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"VZJ_K_39601-20180316_24_G4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "TypeII"
mf["VZJ_K_39601-20180315_20_B1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-600143"
mf["VZJ_K_39601-20180315_20_B1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Gad1-F-600143"
mf["VZJ_K_39601-20180315_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-800078"
mf["VZJ_K_39601-20180315_20_B2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-800078"
mf["VZJ_K_39601-20180315_20_C4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-800078"
mf["VZJ_K_39601-20180316_24_G4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-800078"
# SS01372; 3A;
mf[c("GMR_SS01372-20160226_19_E8-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_SS01372-20160226_19_E8-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS01372-20160226_19_E8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15127-20160226_20_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15127-20160226_20_C8-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15259-20160226_20_B4-Aligned63xScale_2.Smt.SptGraph.swc",
"JRC_SS15259-20160226_20_B4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15259-20160226_20_B4-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "3A"
mf["GMR_SS01372-20160226_19_E8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000427"
mf["GMR_SS01372-20160226_19_E8-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000427"
mf["GMR_SS01372-20160226_19_E8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-200289"
mf["JRC_SS15127-20160226_20_C2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15127-20160226_20_C8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15259-20160226_20_B4-Aligned63xScale_2.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15259-20160226_20_B4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000427"
mf["JRC_SS15259-20160226_20_B4-Aligned63xScale_c1.Smt2.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15293-20151002_19_E1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15293-20151002_19_E2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000427"
mf["JRC_SS15293-20151002_19_E5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15293-20151002_19_E5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-000427"
mf["JRC_SS15293-20151002_19_E6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-300241"
mf["JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300241"
# SS15260, SS22377, SS22730; 16D; Ad1a/f
mf[c("JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H3-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS22730-20160701_22_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22730-20160701_22_E7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H3-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "16D"
# AD1a
mf["JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000258" # Hmm, hoe good is this match really?
mf["JRC_SS22377-20160624_19_G2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22377-20160624_19_G6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22377-20160624_19_H1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22377-20160624_19_H1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22377-20160624_19_H3-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22730-20160701_22_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-400246"
mf["JRC_SS22730-20160701_22_E7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-400246"
# AD1f1
mf["JRC_SS22377-20160624_19_G6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-500032"
# NotLH
mf["JRC_SS22377-20160624_19_G2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-200439"
mf["JRC_SS22377-20160624_19_G6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-200439"
mf["JRC_SS22377-20160624_19_H1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-200439"
mf["JRC_SS22377-20160624_19_H3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-200439"
mf["JRC_SS22377-20160624_19_H3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-200439"
# SS24794; 125; "AV6c1" - New Cell type
mf[c("JRC_SS24794-20160909_25_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24794-20160909_25_B2-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "125"
mf["JRC_SS24794-20160909_25_B1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "AV6c1" # Almost "VGlut-F-100257"
mf["JRC_SS24794-20160909_25_B2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "AV6c1" # Almost "VGlut-F-100257"
# L2220; 154; PV6c - new cell type
mf[c("JRC_SS24172-20160824_31_D1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24172-20160824_31_D1-Aligned63xScale_c1b.Smt2.SptGraph.swc",
"JRC_SS24172-20160824_31_D2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24172-20160824_31_D2-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "154" # PV6?
mf["JRC_SS24172-20160824_31_D1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="PV6c1"
mf["JRC_SS24172-20160824_31_D1-Aligned63xScale_c1b.Smt2.SptGraph.swc",]$match ="PV6c1"
mf["JRC_SS24172-20160824_31_D2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="PV6c1"
mf["JRC_SS24172-20160824_31_D2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="PV6c1"
# 37G11; 11A; PD2a1/b1
mf[c("cell1_GMR_37G11_AE_01-20140618_19_B5-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B6-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B7-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B4-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B7-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B8-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20160624_19_C4-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20160624_19_C5-Aligned63xScale_c0.swc",
"cell1_JRC_SS16059-20160624_19_B3-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B2-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B4-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B6-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20160624_19_C6-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20160624_19_D3-Aligned63xScale_c0.swc",
"cell1_JRC_SS16059-20160624_19_A4-Aligned63xScale_c0.swc",
"cell1_JRC_SS16059-20160624_19_B2-Aligned63xScale_c0.swc",
"cell2_JRC_SS04956-20151125_20_B4-Aligned63xScale_c0.swc",
"cell2_JRC_SS16059-20160624_19_B2-Aligned63xScale_c0.swc",
"cell2_JRC_SS16059-20160624_19_B3-Aligned63xScale_c0.swc",
"cell3_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B3-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B3-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B3-Aligned63xScale_c0.swc",
"cell2_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc"),]$old.cell.type = "11A"
# PD2a1
mf["cell1_GMR_37G11_AE_01-20140618_19_B5-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_GMR_37G11_AE_01-20140618_19_B6-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_GMR_37G11_AE_01-20140618_19_B7-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B7-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B8-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20160624_19_C4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20160624_19_C5-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS16059-20160624_19_B3-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_GMR_37G11_AE_01-20140618_19_B2-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_GMR_37G11_AE_01-20140618_19_B4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B6-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20160624_19_C6-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20160624_19_D3-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS16059-20160624_19_A4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS16059-20160624_19_B2-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell2_JRC_SS04956-20151125_20_B4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell2_JRC_SS16059-20160624_19_B2-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell2_JRC_SS16059-20160624_19_B3-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell3_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
# PD2b1
mf["cell1_JRC_SS04956-20151125_20_B3-Aligned63xScale_c0.swc",]$match ="Cha-F-800096"
mf["cell1_GMR_37G11_AE_01-20140618_19_B3-Aligned63xScale_c0.swc",]$match ="Cha-F-800096"
mf["cell1_JRC_SS04956-20151125_20_B3-Aligned63xScale_c0.swc",]$match ="Cha-F-800096"
mf["cell2_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",]$match ="Cha-F-800096"
# L2444; PN; AL-lALT-PN3
mf[c("GMR_MB583B-20121107_19_H4-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_MB583B-20121107_19_H4-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_MB583B-20121107_19_H4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "PN"
mf["JRC_SS44863-20180209_21_D6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-900038"
# L260; 143; PV1a; Good
mf[c("GMR_MB583B-20121107_19_H4-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_MB583B-20121107_19_H4-Aligned63xScale_c1.Smt5.SptGraph.swc",
"GMR_MB583B-20121107_19_H4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "143"
mf["GMR_MB583B-20121107_19_H4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="TH-M-000042"
mf["GMR_MB583B-20121107_19_H4-Aligned63xScale_c1.Smt5.SptGraph.swc",]$match ="TH-M-000042" # Duplicated
mf["GMR_MB583B-20121107_19_H4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="TH-M-000042" # Duplicated
# L16; 113 and mess; notLHproper
mf[c("GMR_SS00367-20180209_21_H5-Aligned63xScale_c2a.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H5-Aligned63xScale_c2b.Smt2.SptGraph.swc",
"GMR_SS00367-20131220_19_A4-Aligned63xScale_c2a.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H1-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "Input?" # Input type
mf[c("GMR_SS00367-20180209_21_H5-Aligned63xScale_c0a.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H5-Aligned63xScale_c0b.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H1-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H3-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_SS00367-20131220_19_A4-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS00367-20131220_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "113"
mf["GMR_SS00367-20180209_21_H5-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="fru-F-600136"
mf["GMR_SS00367-20180209_21_H5-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="PD2e2" #
mf["GMR_SS00367-20180209_21_H1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="PD2e2"
mf["GMR_SS00367-20180209_21_H3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-F-600136" # Duplicated
mf["GMR_SS00367-20131220_19_A4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="fru-F-600136"
mf["GMR_SS00367-20131220_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-F-600136" # Duplicated
mf["GMR_SS00367-20180209_21_H5-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="fru-M-200431"
mf["GMR_SS00367-20180209_21_H5-Aligned63xScale_c2b.Smt2.SptGraph.swc",]$match ="fru-M-200431"
mf["GMR_SS00367-20131220_19_A4-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="fru-M-200431"
mf["GMR_SS00367-20180209_21_H1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-M-200431"
# L173; 12B; PV5c1
mf[c("JRC_SS03225-20150828_24_F1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_G1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_G1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_G1-Aligned63xScale_c2a.Smt.SptGraph.swc"),]$old.cell.type = "12B"
mf["JRC_SS03225-20150828_24_F1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="E0585-F-300071"
mf["JRC_SS03225-20150828_24_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="E0585-F-300071" # Duplicated
mf["JRC_SS03225-20150828_24_F1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="E0585-F-300071" # Duplicated
mf["JRC_SS03225-20150828_24_F2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000317" # Duplicated
mf["JRC_SS03225-20150828_24_F2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000317"
mf["JRC_SS03225-20150828_24_F2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000317" # Duplicated
mf["JRC_SS03225-20150828_24_G1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-200232"
mf["JRC_SS03225-20150828_24_G1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200232"
mf["JRC_SS03225-20150828_24_G1-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="Gad1-F-200232"
# L1385; 1D; complicated
mf[c("JRC_SS04720-20170623_23_A4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c0b.Smt.SptGraph.swc"),]$old.cell.type = "1D"
mf["JRC_SS04720-20170623_23_A4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="130625c0"
mf["JRC_SS04720-20170623_23_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-000242"
mf["JRC_SS04720-20160819_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-000515" # Investigate further
mf["JRC_SS04720-20160819_21_C1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000515" # Investigate further
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="140618c0" # Investigate further
mf["JRC_SS04720-20160819_21_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-800100" # Investigate further
mf["JRC_SS04720-20170623_23_A2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000515" # Duplicated Investigate further
mf["JRC_SS04720-20170623_23_A2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000515" # Investigate further
mf["JRC_SS04720-20170623_23_B1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20170623_23_A4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200366"
mf["JRC_SS04720-20170623_23_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Duplicated
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Gad1-F-200127" # Investigate further
mf["JRC_SS04720-20160819_21_C3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-600241" # Close, could also be Gad1-F-700106
mf["JRC_SS04720-20170623_23_A7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-400436"
mf["JRC_SS04720-20170623_23_A7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-400436" # Duplicated
mf["JRC_SS04720-20170623_23_A8-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200366"
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Gad1-F-100077"
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-200385"
# L178; 12B; PV5c1
mf[c("JRC_SS04038-20170324_28_C5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04038-20170324_28_C5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04038-20170324_28_C5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04038-20170324_28_C7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "12B"
mf["JRC_SS04038-20170324_28_C5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="E0585-F-400025"
mf["JRC_SS04038-20170324_28_C5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="E0585-F-400025" # Duplicated
mf["JRC_SS04038-20170324_28_C5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="E0585-F-400025" # Duplicated
mf["JRC_SS04038-20170324_28_C7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="E0585-F-400025"
# L258; 54A; PV2a1
mf[c("JRC_SS04955-20151009_19_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B1-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B3-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B3-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54A"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B2-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS04955-20151009_19_B2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="131031c1"
mf["JRC_SS04955-20151009_19_B2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="131031c1"
mf["JRC_SS04955-20151009_19_B3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="5HT1A-M-100027"
mf["JRC_SS04955-20151009_19_B3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="5HT1A-M-100027" # Duplicated
mf["JRC_SS04955-20151009_19_B3-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="5HT1A-M-100027" # Duplicated
mf["JRC_SS04955-20151009_19_B3-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="5HT1A-F-100028" # Duplicated
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="5HT1A-M-100027"
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-300168"
# L421; 1B2; AV4c1
mf[c("JRC_SS04958-20160225_19_C1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C2-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C3-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "1B2"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="fru-F-500093"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="fru-F-500093"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="fru-F-400486"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-F-500093" # Also 131003c1? sort out
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="fru-F-500093" # Also 131003c1? sort out
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="131003c1"
mf["JRC_SS04958-20160225_19_C3-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-F-400486"
# L1828; 29E & 8A;PV4b2 & AD3b1 (# Segmentation: L187; 29E; PV4b1)
mf[c("JRC_SS03773-20180209_21_A7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "29E"
mf[c("JRC_SS03773-20180209_21_A7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "8A"
mf["JRC_SS03773-20180209_21_A7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000533"
mf["JRC_SS03773-20180209_21_A7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-400084"
# L509; 114A; PV4b2 (# Segmentation: not present)
mf[c("JRC_SS03773-20180209_21_A7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03783-20151231_33_A1-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "114A"
mf["JRC_SS03783-20151231_33_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="fru-M-200351"
mf["JRC_SS03783-20151231_33_A1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="fru-M-200351"
# L784; 4B; PV4a5/9
mf[c("JRC_SS03802-20180209_20_A3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03802-20180209_20_A5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03802-20180209_20_A5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A" # What's up with all this?
mf["JRC_SS03802-20180209_20_A3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
# L1467; 4A; PV4a1:6/f1
mf[c("JRC_SS04967-20151022_20_A1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A3-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A7-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A8-Aligned63xScale_c3.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_B1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_B1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS04967-20151022_20_A1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="130703c0" # Check 130925c2? 130219c0? Cha-F-900046?
mf["JRC_SS04967-20151022_20_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-500234"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="130724c0"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="fru-F-400219"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-F-400219" # Duplicated
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="130911c2" # Check, Gad1-F-200395? 130724c0? VGlut-F-700430?
mf["JRC_SS04967-20151022_20_A3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="130625c0"
mf["JRC_SS04967-20151022_20_A3-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="fru-F-400219"
mf["JRC_SS04967-20151022_20_A5-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-400318" # Check, "Gad1-F-000381"?
mf["JRC_SS04967-20151022_20_A5-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Cha-F-500234" # check "130625c0"
mf["JRC_SS04967-20151022_20_A5-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="Cha-F-400318" # Check, "Gad1-F-000381"?
mf["JRC_SS04967-20151022_20_A5-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Gad1-F-000381" # Check, 130625c0? Cha-F-500234?
mf["JRC_SS04967-20151022_20_A7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-500253" # 130625c0 ? Cha-F-500234? 130411c2?
mf["JRC_SS04967-20151022_20_A7-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-500234"
mf["JRC_SS04967-20151022_20_A7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04967-20151022_20_A8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04967-20151022_20_A8-Aligned63xScale_c3.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04967-20151022_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="130704c1" # Check VGlut-F-500253?
mf["JRC_SS04967-20151022_20_B1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="fru-F-500479"
mf["JRC_SS04967-20151022_20_B1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="fru-F-500479" # Duplicated
mf["JRC_SS04967-20151022_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-F-500479" # Duplicated
mf["JRC_SS04967-20151022_20_A3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-600090"
# L1735; 4A; PV4a2/3/5
mf[c("JRC_SS04970-20150828_24_B1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04970-20150828_24_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04970-20150828_24_B1-Aligned63xScale_c3.Smt.SptGraph.swc",
"JRC_SS04970-20150828_24_B5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F7-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F7-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F7-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS04970-20150828_24_B1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04970-20150828_24_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Cha-F-500234"
mf["JRC_SS04970-20150828_24_B1-Aligned63xScale_c3.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04970-20150828_24_B5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="130625c0"
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="130408c0"
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="130408c0" # Duplicated
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04970-20151002_21_F4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04970-20151002_21_F4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="130625c0"
mf["JRC_SS04970-20151002_21_F7-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="VGlut-F-500253" # Gad1-F-500281? 130408c0?
mf["JRC_SS04970-20151002_21_F7-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-100412"
mf["JRC_SS04970-20151002_21_F7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
# L1475; 4A; PV4a2:4
mf[c("JRC_SS04974-20150828_24_H1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20151002_21_E1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20151002_21_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04974-20151002_21_E1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04974-20151002_21_E2-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS04974-20150828_24_H1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000381" # 130411c2
mf["JRC_SS04974-20150828_24_H1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04974-20150828_24_H1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-000381" # 130703c0?
mf["JRC_SS04974-20150828_24_H3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-M-500368"
mf["JRC_SS04974-20150828_24_H3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="fru-M-500368" # Duplicated
mf["JRC_SS04974-20150828_24_H3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-M-500368" # Duplicated, Gad1-F-000381?
mf["JRC_SS04974-20150828_24_H5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04974-20150828_24_H5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04974-20150828_24_H6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04974-20151002_21_E1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Unknown"
mf["JRC_SS04974-20151002_21_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Unknown"
mf["JRC_SS04974-20151002_21_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Unknown"
mf["JRC_SS04974-20151002_21_E2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "130703c0"
# L234; 4A; PV4a1/2
mf[c("JRC_SS15295-20151002_21_A5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15295-20151008_22_B5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15295-20151008_22_B5-Aligned63xScale_c0b.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS15295-20151002_21_A5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "130619c0"
mf["JRC_SS15295-20151008_22_B5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "fru-F-400219"
mf["JRC_SS15295-20151008_22_B5-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "fru-F-400219"
# L954; 4A; PV4a5
mf[c("JRC_SS16060-20151125_19_E7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16060-20151125_19_E7-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS16060-20151125_19_E7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500253"
mf["JRC_SS16060-20151125_19_E7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500253" # Duplicated
# L568; 54A + 1H; PV2a2 + AV4c1/b6
mf[c("JRC_SS16329-20151125_23_A6-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54A"
mf[c("JRC_SS16329-20151125_23_A1-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A6-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "1H"
# PV2a2
mf["JRC_SS16329-20151125_23_A6-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "5HT1A-M-100027"
mf["JRC_SS16329-20151125_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-000242"
# AV4c1/b6
mf["JRC_SS16329-20151125_23_A1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100051"
mf["JRC_SS16329-20151125_23_A1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "Cha-F-400293" # Not a great match...
mf["JRC_SS16329-20151125_23_A6-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "140213c1"
mf["JRC_SS16329-20151125_23_A6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-400293"
# L1473; 4A; PV4a1:4/7/9
mf[c("JRC_SS16345-20151022_20_D2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D3-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D3-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D4-Aligned63xScale_c2.Smt3.SptGraph.swc",
"JRC_SS16345-20151022_20_D5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS16345-20151022_20_D2-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "130205c2" # Check
mf["JRC_SS16345-20151022_20_D2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "130703c0" # Check
mf["JRC_SS16345-20151022_20_D2-Aligned63xScale_c1.Smt2.SptGraph.swc",]$match = "130625c0"
mf["JRC_SS16345-20151022_20_D2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "130411c2"
mf["JRC_SS16345-20151022_20_D3-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "fru-F-500479"
mf["JRC_SS16345-20151022_20_D3-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Cha-F-500234"
mf["JRC_SS16345-20151022_20_D3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "fru-F-400219"
mf["JRC_SS16345-20151022_20_D4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "130625c0"
mf["JRC_SS16345-20151022_20_D4-Aligned63xScale_c2.Smt3.SptGraph.swc",]$match = "130411c2"
mf["JRC_SS16345-20151022_20_D5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-700436" # Check
mf["JRC_SS16345-20151022_20_D5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "fru-F-400219"
mf["JRC_SS16345-20151022_20_D5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "fru-F-400219"
# L542; 4A; PV4a4
mf[c("JRC_SS16652-20170303_25_A2-Aligned63xScale_c0.Smt.SptGraph.swc",
"4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c0.swc",
"4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c1.swc",
"4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c2.swc"),]$old.cell.type = "4A"
mf["JRC_SS16652-20170303_25_A2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "130703c0"
mf["4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c0.swc",]$match ="Cha-F-500234"
mf["4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c1.swc",]$match ="fru-F-400219"
mf["4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c2.swc",]$match ="fru-F-400219"
# L1354; 4A; PV4a3
mf[c("JRC_SS22604-20160729_27_A2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22604-20160729_27_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"4A_JRC_SS22604-20160729_27_A2-Aligned63xScale_c0.swc",
"4A_JRC_SS22604-20160729_27_A2-Aligned63xScale_c1.swc"),]$old.cell.type = "4A"
mf["JRC_SS22604-20160729_27_A2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-000381"
mf["JRC_SS22604-20160729_27_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Gad1-F-000381"
mf["4A_JRC_SS22604-20160729_27_A2-Aligned63xScale_c0.swc",]$match ="VGlut-F-700436"
mf["4A_JRC_SS22604-20160729_27_A2-Aligned63xScale_c1.swc",]$match = "VGlut-F-600752"
# L2013; 54C; PV2a1
mf[c("JRC_SS23347-20170303_26_E2-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "54C"
mf["JRC_SS23347-20170303_26_E2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "131030c0" # not in line?
# L1539; 16B; AD1b1/b2/c1 (# Segmentation 16B; AD1b2)
mf[c("JRC_SS22647-20161007_29_E2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E6-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E6-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E7-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "16B"
mf[c("JRC_SS22647-20161007_29_E2-Aligned63xScale_c0b.Smt.SptGraph.swc"),]$old.cell.type = ""
mf["JRC_SS22647-20161007_29_E2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS22647-20161007_29_E3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS22647-20161007_29_E3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "120726c3"
mf["JRC_SS22647-20161007_29_E6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS22647-20161007_29_E6-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match = "130711c3"
mf["JRC_SS22647-20161007_29_E6-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "120913c1"
mf["JRC_SS22647-20161007_29_E7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120913c1"
mf["JRC_SS22647-20161007_29_E7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "120913c1"
mf["JRC_SS22647-20161007_29_E7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "130711c3"
mf["JRC_SS22647-20161007_29_E2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Gad1-F-200241"
# L1749; 116A & 4A; PD3a1/2/3 & PV4a7; (# Segmentation 116A; PD3a1)
mf[c("JRC_SS22723-20170324_29_F4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F5-Aligned63xScale_c1a.Smt3.SptGraph.swc",
"JRC_SS22723-20170324_29_F2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "116A"
mf[c("JRC_SS22723-20170324_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F5-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "4A"
# PD3
mf["JRC_SS22723-20170324_29_F4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "PD3a4"
mf["JRC_SS22723-20170324_29_F5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "PD3a3"
mf["JRC_SS22723-20170324_29_F4-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "PD3a5"
mf["JRC_SS22723-20170324_29_F5-Aligned63xScale_c1a.Smt3.SptGraph.swc",]$match = "Cha-F-400165"
mf["JRC_SS22723-20170324_29_F2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200150"
# PV4a7
mf["JRC_SS22723-20170324_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F4-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F5-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
# L1328; 138; PV2a1; Good
mf[c("JRC_SS16353-20170303_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "138"
mf["JRC_SS16353-20170303_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-400222"
mf["JRC_SS16353-20170303_21_C2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-400222"
mf["JRC_SS16353-20170303_21_C5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-400222"
mf["JRC_SS16353-20170303_21_C5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-400222" # Duplicated
mf["JRC_SS16353-20170303_21_C6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-400222"
mf["JRC_SS16353-20170303_21_C6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-400222"
# L907; 27A; Av2a1; Good
mf[c("JRC_SS16364-20151217_22_B7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "27A1"
mf["JRC_SS16364-20151217_22_B7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-000240"
# L247; 1B; AV4a2/5
mf[c("JRC_SS16661-20151125_20_F1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c2b.Smt.SptGraph.swc"),]$old.cell.type = "1B1"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-000481"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Cha-F-000481"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-000481"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "Cha-F-000481"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-000079"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "Cha-F-600191"
# L1046; 1B; Av4a2/5/6
mf[c("JRC_SS16786-20151022_19_B3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B6-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B6-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B7-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B7-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "1B1"
mf["JRC_SS16786-20151022_19_B3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-400436" # Av4a5
mf["JRC_SS16786-20151022_19_B4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-000481" # Av4a5
mf["JRC_SS16786-20151022_19_B4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100051" # AV4b5
mf["JRC_SS16786-20151022_19_B6-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "fru-F-600131" # Av4a6
mf["JRC_SS16786-20151022_19_B6-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Gad1-F-700106" # Av4a2
mf["JRC_SS16786-20151022_19_B7-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "Cha-F-000481" # Av4a5
mf["JRC_SS16786-20151022_19_B7-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "fru-F-600131" # Av4a6
mf["JRC_SS16786-20151022_19_B7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-400436" # Av4a5
# L1827; 29E & others; PV4b1/2
mf[c("JRC_SS22732-20180209_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "29E" # Sure??
mf[c("JRC_SS22732-20180209_20_B1-Aligned63xScale_c2b.Smt.SptGraph.swc"),]$old.cell.type = "16F"
mf[c("JRC_SS22732-20180209_20_B2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B5-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B6-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B7-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B7-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "29E"
# PV6b1
mf["JRC_SS22732-20180209_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "PV6b1"
mf["JRC_SS22732-20180209_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "PV6b1"
# AD1d1
mf["JRC_SS22732-20180209_20_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "Gad1-F-300229"
# PV4b1/2
mf["JRC_SS22732-20180209_20_B2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "140117c2"
mf["JRC_SS22732-20180209_20_B4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "140117c2"
mf["JRC_SS22732-20180209_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B5-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B6-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "VGlut-F-400084" # Duplicated
mf["JRC_SS22732-20180209_20_B6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B7-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B7-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "140117c2"
# L629; 27A + 4A; AV2a1/2 + PV4a6 (# Segmentation AV2a1)
mf[c("JRC_SS22737-20160624_20_B3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B3-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B5-Aligned63xScale_c2b.Smt.SptGraph.swc"),]$old.cell.type = "27A"
mf[c("JRC_SS22737-20160624_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
# Av2
mf["JRC_SS22737-20160624_20_B3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B3-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-800214" # Duplicated
mf["JRC_SS22737-20160624_20_B4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B5-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "fru-F-200126"
# PV4
mf["JRC_SS22737-20160624_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200395"
# L1842; 4G; PV4c2
mf[c("JRC_SS23341-20160805_24_A1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "4G"
mf["JRC_SS23341-20160805_24_A1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-100178"
mf["JRC_SS23341-20160805_24_A1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100178" # Duplicated
mf["JRC_SS23341-20160805_24_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-100178" # Duplicated
mf["JRC_SS23341-20160805_24_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-400195"
mf["JRC_SS23341-20160805_24_A4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-400195"
mf["JRC_SS23341-20160805_24_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-400195" # Duplicated
mf["JRC_SS23341-20160805_24_A5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-400195"
mf["JRC_SS23341-20160805_24_A7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-400195"
# L1989; 17C; Av1a1; Good
mf[c("JRC_SS23827-20160902_22_A3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23827-20160902_22_A3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23827-20160902_22_A3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23827-20160902_22_A4-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "17C"
mf["JRC_SS23827-20160902_22_A3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23827-20160902_22_A3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23827-20160902_22_A3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23827-20160902_22_A4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-500105"
# L1990; 17C; Av1a1
mf[c("JRC_SS23828-20160902_22_G1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G7-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "17C"
mf["JRC_SS23828-20160902_22_G1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-200201" # Duplicated
mf["JRC_SS23828-20160902_22_G5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-200201" # Duplicated
mf["JRC_SS23828-20160902_22_G7-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Cha-F-200201"
# L240; 1B; Av4a2/3/5
mf[c("JRC_SS10567-20151008_22_D1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D6-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A1-Aligned63xScale_c0b.Smt2.SptGraph.swc",
"JRC_SS10567-20160408_21_A1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c1a.Smt2.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A4-Aligned63xScale_c0.Smt2.SptGraph.swc",
"JRC_SS10567-20160408_21_A4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "1B1"
mf["JRC_SS10567-20151008_22_D1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300146"
mf["JRC_SS10567-20151008_22_D1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20151008_22_D1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20151008_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20151008_22_D2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-400436"
mf["JRC_SS10567-20151008_22_D2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-400436"
mf["JRC_SS10567-20151008_22_D4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000481"
mf["JRC_SS10567-20151008_22_D4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000481"
mf["JRC_SS10567-20151008_22_D6-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20151008_22_D6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000524"
mf["JRC_SS10567-20151008_22_D7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-400436"
mf["JRC_SS10567-20151008_22_D7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Trh-M-500176"
mf["JRC_SS10567-20160408_21_A1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="Cha-F-600191"
mf["JRC_SS10567-20160408_21_A1-Aligned63xScale_c0b.Smt2.SptGraph.swc",]$match ="Cha-F-000481"
mf["JRC_SS10567-20160408_21_A1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-000481"
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c1a.Smt2.SptGraph.swc",]$match ="Gad1-F-000079" # Duplicated
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000079" # Duplicated
mf["JRC_SS10567-20160408_21_A4-Aligned63xScale_c0.Smt2.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
# L374; 3E; PV5g1/2 (#Segmentation PV5g1)
mf[c("JRC_SS15112-20180209_20_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E1-Aligned63xScale_c1b.Smt2.SptGraph.swc",
"JRC_SS15112-20180209_20_E1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "3E"
mf["JRC_SS15112-20180209_20_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200177"
mf["JRC_SS15112-20180209_20_E1-Aligned63xScale_c1b.Smt2.SptGraph.swc",]$match = "Gad1-F-200177"
mf["JRC_SS15112-20180209_20_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200177"
mf["JRC_SS15112-20180209_20_E2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-200177"
mf["JRC_SS15112-20180209_20_E2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200177" # Duplicated
mf["JRC_SS15112-20180209_20_E5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-300312"
mf["JRC_SS15112-20180209_20_E7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-300312"
mf["JRC_SS15112-20180209_20_E7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-300312" # Duplicated
# L194; 116A; PD3a1 only
mf[c("JRC_SS15256-20151009_19_E1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "116A"
mf["JRC_SS15256-20151009_19_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-500011"
# L259; 54A; PV2a1
mf[c("JRC_SS15285-20150828_23_A1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54A"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "5HT1A-F-100028"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "5HT1A-F-100028"
# L62; 12B 4? 29C; PV6a1
mf[c("JRC_SS15289-20160226_20_F2-Aligned63xScale_c0.Smt2.SptGraph.swc"),]$old.cell.type = "29C"
mf["JRC_SS15289-20160226_20_F2-Aligned63xScale_c0.Smt2.SptGraph.swc",]$match = "CL29CR_30H02"
# L1293; 12A; PV5c1
mf[c("JRC_SS16977-20150828_24_D4-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS16977-20150828_24_D4-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS16977-20150828_24_D4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20150828_24_E1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D3-Aligned63xScale_c3.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "12A"
mf["JRC_SS16977-20150828_24_D4-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20150828_24_D4-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "130814c0" # Check, bad match, 130814c0? 130712c1? 130711c1?
mf["JRC_SS16977-20150828_24_D4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20150828_24_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20151002_21_G2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20151002_21_G2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20151002_21_G4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "130814c0"
mf["JRC_SS16977-20151002_21_G4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "130814c0" # Duplicated
mf["JRC_SS16977-20151002_21_G4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "130814c0" # Duplicated
mf["JRC_SS16977-20151002_21_G7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-000317"
mf["JRC_SS16977-20151002_21_G7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "E0585-F-300071"
mf["JRC_SS16977-20170623_22_D1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "E0585-F-300071"
mf["JRC_SS16977-20170623_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "E0585-F-300071" # Duplicated
mf["JRC_SS16977-20170623_22_D3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "E0585-F-400008"
mf["JRC_SS16977-20170623_22_D3-Aligned63xScale_c3.Smt.SptGraph.swc",]$match = "E0585-F-400008"
mf["JRC_SS16977-20170623_22_D8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-000317"
# L1594; 101; Av4b1; Good
mf[c("JRC_SS16986-20180209_21_B3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16986-20180209_21_B3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "101"
mf["JRC_SS16986-20180209_21_B3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-800067"
mf["JRC_SS16986-20180209_21_B3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-800067" # Duplicated
# L2278; 16B; AD1b2
mf[c("JRC_SS24645-20161007_28_B3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B7-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "16B"
mf["JRC_SS24645-20161007_28_B3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS24645-20161007_28_B4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS24645-20161007_28_B6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS24645-20161007_28_B7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS24645-20161007_28_B7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "120714c4" # Duplicated
mf["JRC_SS24645-20161007_28_B7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "120714c4" # Duplicated
# L2385; 116B; PD3a2
mf[c("JRC_SS24840-20160909_25_F1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24840-20160909_25_F1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "116B"
mf["JRC_SS24840-20160909_25_F1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-200150"
mf["JRC_SS24840-20160909_25_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-200150"
# L876; 116A + 27A; PD3a1/2 + Av2a2/e1
mf[c("JRC_SS25832-20170324_29_D5-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_D5-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_D5-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_E1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_E1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "27A1"
mf[c("JRC_SS25832-20170324_29_D5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_E1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "116A"
mf["JRC_SS25832-20170324_29_D5-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "Cha-F-500105"
mf["JRC_SS25832-20170324_29_D5-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Cha-F-500105"
mf["JRC_SS25832-20170324_29_D5-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "Cha-F-500105"
mf["JRC_SS25832-20170324_29_E1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-500105"
mf["JRC_SS25832-20170324_29_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-500105" # Duplicated
# PD3a
mf["JRC_SS25832-20170324_29_D5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200150"
mf["JRC_SS25832-20170324_29_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-400165"
# L1479; 1H; AV4a1
mf[c("JRC_SS04973-20151125_23_E4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "1H"
mf["JRC_SS04973-20151125_23_E4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-M-700211"
# L979; 29D + others; PV4d3/4 (+ PV1a1 - in image?)
mf[c("JRC_SS04972-20180209_21_F8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F8-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F8-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F5-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "29D"
mf["JRC_SS04972-20180209_21_F8-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-600209"
mf["JRC_SS04972-20180209_21_F8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-600209"
mf["JRC_SS04972-20180209_21_F8-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="130912c1"
mf["JRC_SS04972-20180209_21_F8-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="130912c1"
mf["JRC_SS04972-20180209_21_F5-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Cha-F-600209"
mf["JRC_SS04972-20180209_21_F5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-600209"
mf["JRC_SS04972-20180209_21_F5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-600209"
# Not LH proper
mf["JRC_SS15112-20180209_20_E1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "notLHproper"#"Trh-M-100087"
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS04720-20170623_23_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS10567-20151008_22_D6-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS15112-20180209_20_E5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS16786-20151022_19_B3-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS16786-20151022_19_B3-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS16786-20151022_19_B6-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS16786-20151022_19_B6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS23347-20170303_26_E2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS23347-20170303_26_E2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS24820-20161007_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="notLHproper"
# Mis-registered
mf["JRC_SS03802-20180209_20_A8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS03802-20180209_20_A8-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS03802-20180209_20_A8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS04967-20151022_20_A1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS04967-20151022_20_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS04967-20151022_20_A3-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS22723-20170324_29_F5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS03225-20150828_24_G1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "mis-registered" # Or "131204c0"
mf["JRC_SS03802-20180209_20_A5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "mis-registered" #"130205c2"
mf["JRC_SS03802-20180209_20_A5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "mis-registered" #"130205c2" # Duplicated
# Badly traced
mf["JRC_SS22732-20180209_20_B7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS16329-20151125_23_A6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="mis-registered" # 1H
###################
# Make New Matches #
###################
# If for MCFO skeleton is not, for some reason, in most.lhns
df.a = most.lhns.old[,c("pnt","anatomy.group","cell.type","type")]
df.b = data.frame(pnt = most.lhins.old[,c("tract")],anatomy.group=most.lhins.old[,c("anatomy.group")],cell.type=most.lhins.old[,c("anatomy.group")], type = "IN")
rownames(df.b) = names(most.lhins.old)
df = rbind(df.b,df.a[!rownames(df.a)%in%rownames(df.b),])
mf$pnt = as.character(sapply(mf$match,function(x) df[x,]$pnt))
mf$anatomy.group = as.character(sapply(mf$match,function(x) df[x,]$anatomy.group))
mf$cell.type = as.character(sapply(mf$match,function(x) df[x,]$cell.type))
mf$type = as.character(sapply(mf$match,function(x) df[x,]$type))
#################
# New cell types #
#################
mf[grepl("PV6b1",mf$match),]$pnt = "PV6"
mf[grepl("PV6b1",mf$match),]$anatomy.group = "PV6b"
mf[grepl("PV6b1",mf$match),]$type = "ON"
mf[grepl("PV6b1",mf$match),]$cell.type = "PV6b1"
mf[grepl("PD3a3",mf$match),]$pnt = "PD3"
mf[grepl("PD3a3",mf$match),]$anatomy.group = "PD3a"
mf[grepl("PD3a3",mf$match),]$type = "LN"
mf[grepl("PD3a3",mf$match),]$cell.type = "PD3a3"
mf[grepl("PD3a4",mf$match),]$pnt = "PD3"
mf[grepl("PD3a4",mf$match),]$anatomy.group = "PD3a"
mf[grepl("PD3a4",mf$match),]$type = "LN"
mf[grepl("PD3a4",mf$match),]$cell.type = "PD3a4"
mf[grepl("PD3a5",mf$match),]$pnt = "PD3"
mf[grepl("PD3a5",mf$match),]$anatomy.group = "PD3a"
mf[grepl("PD3a5",mf$match),]$type = "LN"
mf[grepl("PD3a5",mf$match),]$cell.type = "PD3a5"
mf[grepl("PD2e2",mf$match),]$pnt = "PD2"
mf[grepl("PD2e2",mf$match),]$anatomy.group = "PD2e"
mf[grepl("PD2e2",mf$match),]$type = "ON"
mf[grepl("PD2e2",mf$match),]$cell.type = "PD2e2"
mf[grepl("AV6c1",mf$match),]$pnt = "AV6"
mf[grepl("AV6c1",mf$match),]$anatomy.group = "AV6c"
mf[grepl("AV6c1",mf$match),]$type = "ON"
mf[grepl("AV6c1",mf$match),]$cell.type = "AV6c1"
mf[grepl("PV6a3",mf$match),]$pnt = "PV6"
mf[grepl("PV6a3",mf$match),]$anatomy.group = "PV6a"
mf[grepl("PV6a3",mf$match),]$type = "ON"
mf[grepl("PV6a3",mf$match),]$cell.type = "PV6a3"
mf[grepl("AV4f1",mf$match),]$pnt = "AV4"
mf[grepl("AV4f1",mf$match),]$anatomy.group = "AV4f"
mf[grepl("AV4f1",mf$match),]$type = "ON"
mf[grepl("AV4f1",mf$match),]$cell.type = "AV4f1"
mf[grepl("PV6c1",mf$match),]$pnt = "PV6"
mf[grepl("PV6c1",mf$match),]$anatomy.group = "PV6c"
mf[grepl("PV6c1",mf$match),]$type = "ON"
mf[grepl("PV6c1",mf$match),]$cell.type = "PV6c1"
mf[grepl("WED-PN3",mf$match),]$pnt = "WEDT"
mf[grepl("WED-PN3",mf$match),]$anatomy.group = "WED-PN"
mf[grepl("WED-PN3",mf$match),]$type = "IN"
mf[grepl("WED-PN3",mf$match),]$cell.type = "WED-PN3"
mf[grepl("WED-PN5",mf$match),]$pnt = "WEDT"
mf[grepl("WED-PN5",mf$match),]$anatomy.group = "WED-PN"
mf[grepl("WED-PN5",mf$match),]$type = "IN"
mf[grepl("WED-PN5",mf$match),]$cell.type = "WED-PN5"
mf[grepl("AD1d1",mf$match),]$pnt = "AD1"
mf[grepl("AD1d1",mf$match),]$anatomy.group = "AD1d"
mf[grepl("AD1d1",mf$match),]$type = "ON"
mf[grepl("AD1d1",mf$match),]$cell.type = "AD1d1"
mf[grepl("MB-C1",mf$match),]$pnt = "PV2"
mf[grepl("MB-C1",mf$match),]$anatomy.group = "MB-LH"
mf[grepl("MB-C1",mf$match),]$type = "ON"
mf[grepl("MB-C1",mf$match),]$cell.type = "MB-C1"
###################################################
# Mike Dolan determines what is in exemplar lines #
###################################################
mf[,"InLine"] = TRUE
mf[c("JRC_SS22723-20170324_29_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS23347-20170303_26_E2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03773-20180209_21_A7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS21811-20161007_29_B7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03773-20180209_21_A7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A6-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16564-20160311_23_D7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22730-20160701_22_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22730-20160701_22_E7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A6-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E3-Aligned63xScale_c1.Smt.SptGraph.swc"
),"InLine"] = FALSE
#############
# Save data #
#############
mf$neurotransmitter = as.character(sapply(mf[,"old.cell.type"],function(x) subset(stainings,old.cell.type==x)$NT[1]))
mf$cell.number = as.character(sapply(mf[,"old.cell.type"],function(x) subset(stainings,old.cell.type==x)$no.cells[1]))
mf$coreLH = FALSE
lh.mcfo = mcfo
order = order(mf$linecode)
mf = mf[order,]
lh.mcfo = lh.mcfo[order]
r <- rle(as.character(mf$linecode))
rownames(mf) = names(lh.mcfo) = paste0(rep(r$values, times = r$lengths), "#",unlist(lapply(r$lengths, seq_len)))
mf = mf[,-3]
attr(lh.mcfo,"df") = mf
################
# Make Matches #
################
# Synchronise with most.lhns
most.lh = nat::union(most.lhns.old,most.lhins.old)
in.most.lhns = names(lh.mcfo)[names(lh.mcfo)%in%names(most.lh)]
lh.mcfo[in.most.lhns,c("pnt","anatomy.group","cell.type","type","coreLH")] = most.lh[in.most.lhns,c("pnt","anatomy.group","cell.type","type","coreLH")]
lh.mcfo[,"id"] = names(lh.mcfo)
# remove non=ASCII chracter
lh.mcfo[,] = change_nonascii(lh.mcfo[,])
jefferislab/lhns documentation built on Aug. 20, 2020, 10:10 p.m.
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##################################
# Read and process MCFO skeletons #
#################################
# Prepare data on Mike's splits
if(!exists("most.lhns")){
stop("Please run processLHNs.R!")
}else if(!exists("most.lhins")){
stop("Please run processLHNinputs.R!")
}
most.lhns.old = most.lhns
most.lhins.old = most.lhins
# Use olf Frechter et al. names for this file
if(!is.null(most.lhns.old[,"frechter.cell.type"])){
most.lhns.old[,"cell.type"] = most.lhns.old[,"frechter.cell.type"]
}
if(!is.null(most.lhins.old[,"frechter.cell.type"])){
most.lhins.old[,"cell.type"] = most.lhins.old[,"frechter.cell.type"]
}
# # Read MCFO neurons
# mcfo = read.neurons("/Users/abates/ImageData/MCFO/lastish_stacks/skels4")
# mcfo = nlapply(mcfo,nat::resample, stepsize = 1)
#
# # Fix skeletons (fix a few issues with Amira skeletons, like loops and star-burst node connectivity)
# nl = nat::neuronlist()
# for(mn in mcfo){
# file = names(mcfo)[length(nl)+1]
# message(length(nl)+1)
# x = nat::xyzmatrix(mn)
# k = 10
# swc = data.frame(PointNo = 1:nrow(x),Label = 0,x,W = -2, Parent = -1, tree = NA) # Create SWC data.frame
# nears = nabor::knn(data = x, query = x, k = k) # Find the closest k nodes
# all.dists = nabor::knn(data = x, query = x, k = nrow(x)) # Find the closest k nodes
# skel = 1 # We will grow our tree from, as start, the root for the first skeleton as the first point
# used = c()
# d = 0.1 #mean(nears[[2]][,-1]) # Start with the smallest connection distance, then grow the connection distance to its maximum. dd is the lower bound.
# distance.steps = 0.1
# connection.distance = 100 #max(nears[[2]][,c(2,3)]) # Max distance by which nodes can be connected
# parents = nears[[1]][,-1][which.min(all.dists[[2]][,-1])] # Start with a faux 'root'
# used = c()
# print(d)
# while(sum(is.na(swc$tree))>0) {
# if(all(parents%in%used)){ # If we run out of nodes in the connection range
# skel = skel + 1; leaves = c()
# dists = nears[[2]][-1*used,-1]
# indices = nears[[1]][-1*used,-1]
# parents = indices[which.min(dists)]
# parents = subset(swc,is.na(tree))$PointNo[[1]]
# }
# search = nears[[1]]; search[!nears[[2]]<=d] = NA # Get the closest matches in space to each non-zero point in the image stack
# used = c(used,parents) # Parent nodes cannot be assigned to matches already within the tree
# children = search[parents,]# Find the right match row
# children = unique(children[!is.na(children)]) # Get children, i.e. candidate child nodes, within the connection distance
# children = children[!children%in%used] # Remove the nodes we have already added to our skeleton
# swc[unique(c(parents,children)),"tree"] = skel # So now we'll assign them to a skeleton
# if(length(children[!is.na(children)])>0){ # If there are children
# if(length(children)>1){
# closest.parents = apply(search[children,],1, function(x) x[x%in%parents][1])
# if(sum(is.na(closest.parents))>0){ # The the closest parent is not within the top k matches, look the other way
# lost = children[is.na(closest.parents)]
# closest.parents[is.na(closest.parents)] = sapply(lost,function(x) rep(parents,k)[which.max(search[parents,]==x)[1]])
# }
# }else{
# closest.parents = search[children,][search[children,]%in%parents][1]
# if(sum(is.na(closest.parents))>0){ # The the closest parent is not within the top k matches, look the other way
# closest.parents = rep(parents,k)[which.max(search[parents,]==children)][1]
# }
# }
# swc[children,"Parent"] = closest.parents # Assign to the closest parent
# parents = children # Now grow tree from the old children
# }
# }
# # Now we have created a bunch of skeletons at the minimal connection distance, d.
# # We need to grow our search aread to d.max and so merge these different skeletons
# dd = d # Minimal
# d = d + distance.steps # Maximal
# while(d<=connection.distance){
# # Get the indices within the search distance
# print(d)
# search = nears[[1]]
# search[!nears[[2]]<=d] = NA
# search[!nears[[2]]>dd] = NA
# # Get the distances
# dists = nears[[2]]
# m = reshape2::melt(dists)
# m = subset(m,value<=d)
# m = subset(m,value>dd)
# # Order indices to grow by shortest distance to next node
# m = m[order(m$value),]
# for(parent in m$Var1){
# t = swc[parent,"tree"]
# used = subset(swc,tree==t)$PointNo
# children = search[parent,]# Find the right match row
# children = unique(children[!is.na(children)]) # Get children, i.e. candidate child nodes, within the connection distance
# children = children[!children%in%used] # Remove the nodes we have already added to our tree
# children = children[!duplicated(swc[children,"tree"])] # Children must be in different trees from one another
# if(length(children)>0){
# for(child in children){ # Now combine the trees
# child.tree = swc[as.character(child),"tree"]
# n = subset(swc,tree==child.tree)
# if(nrow(n)>1){ # Connect another tree
# n = nat::as.neuron(nat::as.ngraph(n), origin = child)$d
# # el = n[n$Parent != -1, c("Parent", "PointNo")]
# # el = el[el$Parent%in%n$PointNo,]
# # n = ngraph(data.matrix(el), n$PointNo, directed = TRUE, xyz = xyzmatrix(n), diam = n$W)
# # n = nat::as.neuron(n)$d
# n$tree = t
# n[n$PointNo==child,"Parent"] = parent
# swc[n$PointNo,] = n
# }else if (nrow(n)==1){ # Connect isolated node
# n$tree = t
# swc[swc$PointNo==child,"Parent"] = parent
# swc[as.character(n$PointNo),"tree"] = t
# }
# }
# }
# }
# # Increase the search distance
# dd = d # New min
# d = d + distance.steps # New max
# }
# isolated = sapply(swc$PointNo,function(x) (!x%in%swc$Parent)&(swc[x,"Parent"]==-1))
# swc = swc[!isolated,] # Remove isolated nodes
# swc = swc[!is.na(swc$PointNo),]
# nn = nat::as.neuron(swc)
# nams = c(names(nl),file)
# nl = c(nl,nat::as.neuronlist(nn))
# names(nl) = nams
# }
# attr(nl,"df") = data.frame(file=names(mcfo))
# nl = nlapply(nl,nat::resample, stepsize = 1)
# names(nl) = as.character(nl[,"file"])
#
# # Fit soma - interactive
# nl = catnat::correctsoma(nl)
# names(nl) = as.character(nl[,"file"])
#
# # Flip neurons - interactive
# nopen3d();plot3d(nl,soma=T);plot3d(JFRC2013)
# left.side.neurons = nat::find.soma(db=nl)
# nl[left.side.neurons] = mirror_brain(nl[left.side.neurons],brain = JFRC2013)
#
#
# # Transform to FCWB space
# mcfo4 = nat::nlapply(nl,nat.templatebrains::xform_brain,sample = nat.flybrains::JFRC2013,reference= nat.flybrains::FCWB,OmitFailures = T) # any lost?
# # # save
# # save(mcfo,file = "data-raw/dolan_mcfo.rda")
#################################
# Meta-data for the MCFO object #
#################################
# Load data
load("data-raw/dolan_mcfo.rda")
for(i in 1:length(mcfo)){
mcfo[[i]]$d$Label = 0
}
# Detect and remove duplicated skeletons
# Get the imade code to line mapping
dcs = read.csv("data-raw/csv/dolan_cells.csv")
dcs$ImageCode = NULL
dcs = aggregate(No_Cells ~ LineCode + old.cell.type, dcs, function(x) paste0(round(mean(x)),ifelse(!is.na(sd(x)),paste0("±",round(sd(x))),"")))
colnames(dcs) = c("LineCode","old.cell.type","no.cells")
nts = read.csv("data-raw/csv/NT_annotation_from_Mike.csv")
stainings = merge(dcs,nts,all.x=TRUE,all.y=TRUE)
codes = read.csv("data-raw/csv/FlycoreCodes.csv")
s = as.character(codes[,"Genotype"])
# Work out metadata
d = read.csv("data-raw/csv/SplitGAL4annotate.csv",header = TRUE)
colnames(d) = c("linecode","imagecode","AD","DBD","old.cell.type","num.lh.clusters","Ideal","Behaviour","MCFO","Polarity","Stablestock","VNC","ImagePath")
d$imagecode = NULL
d = d[!duplicated(d$linecode),]
rownames(d) = d$linecode
m = c();lines = c(); nams = c()
for(nam in names(mcfo)){
n = gsub("^4a_","",nam)
n = gsub("^cell1_","",n)
n = gsub("*-.*","",n)
n = gsub(".*_","",n)
if(n=="01"){
n="37G11"
}
mch = match(n,s)
lines = c(lines,ifelse(is.na(mch),n,as.character(codes[mch,"LineCode"])))
m = c(m,mch)
nams = c(nams, n)
}
#mf = data.frame(linecode = codes[m,"LineCode"])
mf = data.frame(linecode = as.character(lines))
mf$genotype = codes[m,"Genotype"]
mf = cbind(mf,d[as.character(mf$linecode),])
mf[,c("pnt","anatomy.group","cell.type","type")] = "notLHproper"
mf$match = NA
mf$skeleton.type = "MCFO"
mf$file = rownames(mf) = names(mcfo)
mf[] = lapply(mf, as.character)
mf = mf[,!colnames(mf)%in%c("linecode.1","ImagePath")]
# # NBlast
# mcfo.dps = dotprops(mcfo,resample=1)
# result1 = nblast(mcfo.dps, c(lhns::most.lhns.dps,lhns::most.lhins.dps))
# result2 = nblast(c(lhns::most.lhns.dps,lhns::most.lhins.dps), mcfo.dps)
# result = (result1 + t(result2))/2
# most.lh = c(lhns::most.lhns,lhns::most.lhins)
# for(c in 1:ncol(result)){
# clear3d()
# plot3d(FCWB)
# message(paste0(c,"/",ncol(result)))
# message(names(mcfo[c]))
# plot3d(mcfo[c],col = "black",lwd=3,soma=T)
# n = nlscan(most.lh[names(sort(result[,c],decreasing = TRUE))],col="red",lwd=2,soma=T)
# }
##############################
# Assignments to LHN library #
##############################
# L1477; 4A
mf[c("JRC_SS22624-20160701_21_D6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22624-20160701_21_D7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22624-20160701_21_D8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf[c("JRC_SS22624-20160701_21_D6-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Cha-F-100412"
mf[c("JRC_SS22624-20160701_21_D7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "VGlut-F-500253"
mf[c("JRC_SS22624-20160701_21_D8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "VGlut-F-600752"
# L1721; 16C
mf[c("JRC_SS22713-20160624_20_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22713-20160624_20_C6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22713-20160624_20_C7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "16C"
mf[c("JRC_SS22713-20160624_20_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22713-20160624_20_C6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22713-20160624_20_C7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "Cha-F-400246"
# L2033; 145
mf[c("JRC_SS23107-20160701_22_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23107-20160701_22_C5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "145"
mf[c("JRC_SS23107-20160701_22_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23107-20160701_22_C5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Gad1-F-600202"
# L2098; 1A
mf[c("JRC_SS23129-20160805_24_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23129-20160805_24_C4-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$old.cell.type = "1A2"
mf[c("JRC_SS23129-20160805_24_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23129-20160805_24_C4-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$match = "Gad1-F-200366"
# L2233; 4E
mf[c("JRC_SS23187-20160805_23_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F7-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$old.cell.type = "4E"
mf[c("JRC_SS23187-20160805_23_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23187-20160805_23_F7-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$match = "Cha-F-200398"
# L1959; 29G
mf[c("JRC_SS23354-20160909_25_H1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "29G"
mf[c("JRC_SS23354-20160909_25_H1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "VGlut-F-500445"
# L1847; 54C
mf[c("JRC_SS23805-20160902_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54C"
mf[c("JRC_SS23805-20160902_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-800092"
# L1900; 85
mf[c("JRC_SS23817-20170623_24_B1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "85"
mf[c("JRC_SS23817-20170623_24_B1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "MB-C1"
# L452; 27C
mf[c("JRC_SS22532-20160928_31_C1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "27C"
mf[c("JRC_SS22532-20160928_31_C1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22532-20160928_31_C2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-500140"
# MB036B;
mf[c("GMR_MB036B-20151217_22_C2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "3C"
mf[c("GMR_MB036B-20151217_22_C2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Cha-F-800045"
# MB072C;
mf[c("GMR_MB072C-20151105_25_E2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "120"
mf[c("GMR_MB072C-20151105_25_E2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "fru-M-000360"
# fru-M-000179
# SS01371;
mf[c("GMR_SS01371-20151105_25_C7-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS01371-20151105_25_D6-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "16A"
mf[c("GMR_SS01371-20151105_25_C7-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS01371-20151105_25_D6-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "AD1d1"
# L163;
mf[c("JRC_SS03224-20150828_23_B5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03224-20151002_21_C3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "3D"
mf[c("JRC_SS03224-20150828_23_B5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03224-20151002_21_C3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Cha-F-500250"
# L528;
mf[c("JRC_SS03237-20151015_19_D2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "141"
mf[c("JRC_SS03237-20151015_19_D2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-300290"
# L849;
mf[c("JRC_SS04948-20151217_26_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04948-20151217_26_B5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "3F"
mf[c("JRC_SS04948-20151217_26_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04948-20151217_26_B5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Cha-F-300342"
# L19;
mf[c("JRC_SS06600-20151002_20_B3-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "8A"
mf[c("JRC_SS06600-20151002_20_B3-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Cha-F-000533"
# L20;
mf[c("JRC_SS15113-20151009_19_C4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "8A"
mf[c("JRC_SS15113-20151009_19_C4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Cha-F-000533"
# L304;
mf[c("JRC_SS15279-20170303_21_B4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "8A"
mf[c("JRC_SS15279-20170303_21_B4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "Cha-F-000533"
# L85;
mf[c("JRC_SS15297-20151002_20_C2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15297-20151002_20_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15297-20151002_20_C8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15297-20161028_17_A1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15297-20161028_17_A1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "51B"
mf[c("JRC_SS15297-20151002_20_C2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15297-20151002_20_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15297-20151002_20_C8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15297-20161028_17_A1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Cha-F-000086"
mf[c("JRC_SS15297-20161028_17_A1-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "Cha-F-000086" # Almost, but not quite...
# L1397;
mf[c("JRC_SS16027-20151022_19_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16027-20151022_19_E1-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS16027-20151022_19_E5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "29G"
mf[c("JRC_SS16027-20151022_19_E1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "VGlut-F-500445"
mf[c("JRC_SS16027-20151022_19_E1-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$match ="VGlut-F-900028"
mf[c("JRC_SS16027-20151022_19_E5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "VGlut-F-900028"
# L787;
mf[c("JRC_SS16564-20160311_23_D7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16564-20160311_23_D7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16564-20160311_23_D8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "1A"
mf[c("JRC_SS16564-20160311_23_D7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$match = "Gad1-F-200366" # OR Gad1-F-200155
mf[c("JRC_SS16564-20160311_23_D7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "AV4f1"
mf[c("JRC_SS16564-20160311_23_D8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-200366" # OR Gad1-F-200155
# L494;
mf[c("JRC_SS16659-20170303_25_B2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16659-20170303_25_B5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "16A2"
mf[c("JRC_SS16659-20170303_25_B2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16659-20170303_25_B5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Gad1-F-500014"
# L1554;
mf[c("JRC_SS22656-20160701_22_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22656-20160701_22_F8-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "3C"
mf[c("JRC_SS22656-20160701_22_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22656-20160701_22_F8-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "Cha-F-800045"
# L1614;
mf[c("JRC_SS22675-20160624_20_A1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "16F"
mf[c("JRC_SS22675-20160624_20_A1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "fru-F-300009"
# L1900;
mf[c("JRC_SS23817-20170623_24_B4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "85"
mf[c("JRC_SS23817-20170623_24_B4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "MB-C1"
# L1955;
mf[c("JRC_SS23824-20160909_26_A4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54C"
mf[c("JRC_SS23824-20160909_26_A4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-800092"
# L2087;
mf[c( "JRC_SS24177-20160909_26_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24177-20160909_26_F4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24177-20160909_26_F4-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS24177-20160909_26_F5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "84"
mf[c( "JRC_SS24177-20160909_26_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24177-20160909_26_F4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24177-20160909_26_F4-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS24177-20160909_26_F5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "Gad1-F-300218"
# L2088;
mf[c("JRC_SS24659-20161104_18_A2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24659-20161104_18_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24659-20161104_18_A2-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "84"
mf[c("JRC_SS24659-20161104_18_A2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24659-20161104_18_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24659-20161104_18_A2-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$match = "Gad1-F-300218"
# L2392;
mf[c("JRC_SS24820-20161007_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt3.SptGraph.swc"),]$old.cell.type = "76B"
mf[c("JRC_SS24820-20161007_29_F1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS24820-20161007_29_F6-Aligned63xScale_c2.Smt3.SptGraph.swc"),]$match = "VGlut-F-400240"
# L2316;
mf[c("JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "76B"
mf[c("JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$match = "VGlut-F-700280"
# L475;
mf[c( "JRC_SS30939-20161007_30_B7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS30939-20161007_30_B7-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$old.cell.type = "16A2"
mf[c( "JRC_SS30939-20161007_30_B7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS30939-20161007_30_B7-Aligned63xScale_c1.Smt2.SptGraph.swc"),]$match = "Gad1-F-300262"
# L1668; 70A
mf[c("JRC_SS03791-20151105_24_E2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03791-20151105_24_E2-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS03791-20151105_24_E3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03791-20151105_24_E6-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "70A"
mf[c("JRC_SS03791-20151105_24_E2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03791-20151105_24_E2-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS03791-20151105_24_E3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03791-20151105_24_E6-Aligned63xScale_c1.Smt.SptGraph.swc"),]$match = "WED-PN3"
# L1518; 70A
mf[c("JRC_SS03801-20151125_19_B2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70A"
mf[c("JRC_SS03801-20151125_19_B2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03801-20151125_19_B6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "WED-PN3"
# L1129; 7A
mf[c("JRC_SS04950-20170303_21_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04950-20170303_21_A2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04950-20170303_21_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04950-20170303_21_A5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04950-20170303_21_A6-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "7A"
mf["JRC_SS04950-20170303_21_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-600143"
mf["JRC_SS04950-20170303_21_A2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-600143"
mf["JRC_SS04950-20170303_21_A2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-800078"
mf["JRC_SS04950-20170303_21_A5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-800082"
mf["JRC_SS04950-20170303_21_A6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-600143"
# L1129; 70C
mf[c("JRC_SS04961-20151217_26_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04961-20151217_26_E8-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "70C"
mf["JRC_SS04961-20151217_26_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS04961-20151217_26_E8-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match = "VGlut-F-500810"
# L1337; 70B
mf[c("JRC_SS04962-20151125_23_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70B"
mf[c("JRC_SS04962-20151125_23_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04962-20151125_23_F8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "WED-PN5"
# L452; 70A
mf[c("JRC_SS15280-20151015_19_G1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15280-20151015_19_G4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15280-20151015_19_G4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70A"
mf[c("JRC_SS15280-20151015_19_G1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15280-20151015_19_G4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15280-20151015_19_G4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "WED-PN3"
# L788; 1D
mf[c("JRC_SS16038-20151125_23_G1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16038-20151125_23_G1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16038-20151125_23_G1-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "1D"
mf["JRC_SS16038-20151125_23_G1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "fru-F-700136"
mf["JRC_SS16038-20151125_23_G1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "fru-F-700136"
mf["JRC_SS16038-20151125_23_G1-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match = "fru-F-700136"
# L112; 7OC
mf[c("JRC_SS16337-20151125_20_D4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16337-20151125_20_D5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16337-20151125_20_D7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16337-20151125_20_D8-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "7OC"
mf["JRC_SS16337-20151125_20_D4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS16337-20151125_20_D5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS16337-20151125_20_D7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
mf["JRC_SS16337-20151125_20_D8-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500810"
# L1117; 7A
mf[c("JRC_SS16351-20160819_23_C4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "7A"
mf["JRC_SS16351-20160819_23_C4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-500832" # Not in line
mf["JRC_SS16351-20160819_23_C4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-600143"
mf["JRC_SS16351-20160819_23_C6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-200185"
# L271; 7A
mf[c("JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS21811-20161007_29_B7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B8-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "7A"
mf["JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-200185"
mf["JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match ="Cha-F-200185"
mf["JRC_SS21811-20161007_29_B7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-800082"
mf["JRC_SS21811-20161007_29_B8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-200185"
# L1524; 70D;
mf[c("JRC_SS22640-20161007_30_D3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22640-20161007_30_D3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22640-20161007_30_D5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22640-20161007_30_D8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "70D"
mf["JRC_SS22640-20161007_30_D3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000514"
mf["JRC_SS22640-20161007_30_D3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000514"
mf["JRC_SS22640-20161007_30_D5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000514"
mf["JRC_SS22640-20161007_30_D8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000514"
# L770 ; 70C
mf[c("JRC_SS22763-20170324_30_A3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22763-20170324_30_A3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70C"
mf["JRC_SS22763-20170324_30_A3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-500810"
mf["JRC_SS22763-20170324_30_A3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500810"
# L772; 70C
mf[c("JRC_SS22764-20170428_25_C3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22764-20170428_25_C8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "70C"
mf["JRC_SS22764-20170428_25_C3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500810"
mf["JRC_SS22764-20170428_25_C8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500810"
# L2001; 147
mf[c("JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt3.SptGraph.swc",
"JRC_SS23097-20160624_20_F3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23097-20160624_20_F8-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "147"
mf["JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F2-Aligned63xScale_c2.Smt3.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23097-20160624_20_F8-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match = "Gad1-F-200237"
# L2002; 147
mf[c("JRC_SS23098-20160805_24_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23098-20160805_24_B6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "147"
mf["JRC_SS23098-20160805_24_B4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
mf["JRC_SS23098-20160805_24_B6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200237"
# L2185; 29B
mf[c("JRC_SS23170-20160805_23_D3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23170-20160805_23_D6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "29B"
mf[c("JRC_SS23170-20160805_23_D3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23170-20160805_23_D6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "PV6a3"
# 70A: L1949
mf[c("JRC_SS23376-20170324_28_D3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23376-20170324_28_D5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23376-20170324_28_D5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "70A"
mf[c("JRC_SS23376-20170324_28_D3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23376-20170324_28_D5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23376-20170324_28_D5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$match = "WED-PN3"
# L2193; 29B
mf[c("JRC_SS24679-20161104_18_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B5-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS24679-20161104_18_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B6-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$old.cell.type = "29B"
mf[c("JRC_SS24679-20161104_18_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B5-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS24679-20161104_18_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24679-20161104_18_B6-Aligned63xScale_c2.Smt2.SptGraph.swc"),]$match = "PV6a3"
# NP6099; TypeII
mf[c("VZJ_K_39601-20180315_20_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"VZJ_K_39601-20180315_20_B1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"VZJ_K_39601-20180315_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"VZJ_K_39601-20180315_20_B2-Aligned63xScale_c0.Smt.SptGraph.swc",
"VZJ_K_39601-20180315_20_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"VZJ_K_39601-20180316_24_G4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "TypeII"
mf["VZJ_K_39601-20180315_20_B1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-600143"
mf["VZJ_K_39601-20180315_20_B1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Gad1-F-600143"
mf["VZJ_K_39601-20180315_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-800078"
mf["VZJ_K_39601-20180315_20_B2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-800078"
mf["VZJ_K_39601-20180315_20_C4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-800078"
mf["VZJ_K_39601-20180316_24_G4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-800078"
# SS01372; 3A;
mf[c("GMR_SS01372-20160226_19_E8-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_SS01372-20160226_19_E8-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS01372-20160226_19_E8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15127-20160226_20_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15127-20160226_20_C8-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15259-20160226_20_B4-Aligned63xScale_2.Smt.SptGraph.swc",
"JRC_SS15259-20160226_20_B4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15259-20160226_20_B4-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15293-20151002_19_E6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "3A"
mf["GMR_SS01372-20160226_19_E8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000427"
mf["GMR_SS01372-20160226_19_E8-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000427"
mf["GMR_SS01372-20160226_19_E8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-200289"
mf["JRC_SS15127-20160226_20_C2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15127-20160226_20_C8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15259-20160226_20_B4-Aligned63xScale_2.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15259-20160226_20_B4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000427"
mf["JRC_SS15259-20160226_20_B4-Aligned63xScale_c1.Smt2.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15293-20151002_19_E1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15293-20151002_19_E2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000427"
mf["JRC_SS15293-20151002_19_E5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-300241"
mf["JRC_SS15293-20151002_19_E5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-000427"
mf["JRC_SS15293-20151002_19_E6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-300241"
mf["JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300241"
# SS15260, SS22377, SS22730; 16D; Ad1a/f
mf[c("JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H3-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS22730-20160701_22_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22730-20160701_22_E7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_G6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22377-20160624_19_H3-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "16D"
# AD1a
mf["JRC_SS15260-20151008_23_D4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000258" # Hmm, hoe good is this match really?
mf["JRC_SS22377-20160624_19_G2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22377-20160624_19_G6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22377-20160624_19_H1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22377-20160624_19_H1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22377-20160624_19_H3-Aligned63xScale_c2.Smt2.SptGraph.swc",]$match ="Cha-F-000258"
mf["JRC_SS22730-20160701_22_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-400246"
mf["JRC_SS22730-20160701_22_E7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-400246"
# AD1f1
mf["JRC_SS22377-20160624_19_G6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-500032"
# NotLH
mf["JRC_SS22377-20160624_19_G2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-200439"
mf["JRC_SS22377-20160624_19_G6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-200439"
mf["JRC_SS22377-20160624_19_H1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-200439"
mf["JRC_SS22377-20160624_19_H3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-200439"
mf["JRC_SS22377-20160624_19_H3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-200439"
# SS24794; 125; "AV6c1" - New Cell type
mf[c("JRC_SS24794-20160909_25_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS24794-20160909_25_B2-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "125"
mf["JRC_SS24794-20160909_25_B1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "AV6c1" # Almost "VGlut-F-100257"
mf["JRC_SS24794-20160909_25_B2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "AV6c1" # Almost "VGlut-F-100257"
# L2220; 154; PV6c - new cell type
mf[c("JRC_SS24172-20160824_31_D1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24172-20160824_31_D1-Aligned63xScale_c1b.Smt2.SptGraph.swc",
"JRC_SS24172-20160824_31_D2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24172-20160824_31_D2-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "154" # PV6?
mf["JRC_SS24172-20160824_31_D1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="PV6c1"
mf["JRC_SS24172-20160824_31_D1-Aligned63xScale_c1b.Smt2.SptGraph.swc",]$match ="PV6c1"
mf["JRC_SS24172-20160824_31_D2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="PV6c1"
mf["JRC_SS24172-20160824_31_D2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="PV6c1"
# 37G11; 11A; PD2a1/b1
mf[c("cell1_GMR_37G11_AE_01-20140618_19_B5-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B6-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B7-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B4-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B7-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B8-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20160624_19_C4-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20160624_19_C5-Aligned63xScale_c0.swc",
"cell1_JRC_SS16059-20160624_19_B3-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B2-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B4-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B6-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20160624_19_C6-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20160624_19_D3-Aligned63xScale_c0.swc",
"cell1_JRC_SS16059-20160624_19_A4-Aligned63xScale_c0.swc",
"cell1_JRC_SS16059-20160624_19_B2-Aligned63xScale_c0.swc",
"cell2_JRC_SS04956-20151125_20_B4-Aligned63xScale_c0.swc",
"cell2_JRC_SS16059-20160624_19_B2-Aligned63xScale_c0.swc",
"cell2_JRC_SS16059-20160624_19_B3-Aligned63xScale_c0.swc",
"cell3_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B3-Aligned63xScale_c0.swc",
"cell1_GMR_37G11_AE_01-20140618_19_B3-Aligned63xScale_c0.swc",
"cell1_JRC_SS04956-20151125_20_B3-Aligned63xScale_c0.swc",
"cell2_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc"),]$old.cell.type = "11A"
# PD2a1
mf["cell1_GMR_37G11_AE_01-20140618_19_B5-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_GMR_37G11_AE_01-20140618_19_B6-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_GMR_37G11_AE_01-20140618_19_B7-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B7-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B8-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20160624_19_C4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20160624_19_C5-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS16059-20160624_19_B3-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_GMR_37G11_AE_01-20140618_19_B2-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_GMR_37G11_AE_01-20140618_19_B4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20151125_20_B6-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20160624_19_C6-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS04956-20160624_19_D3-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS16059-20160624_19_A4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell1_JRC_SS16059-20160624_19_B2-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell2_JRC_SS04956-20151125_20_B4-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell2_JRC_SS16059-20160624_19_B2-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell2_JRC_SS16059-20160624_19_B3-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
mf["cell3_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",]$match ="5HT1A-F-300019"
# PD2b1
mf["cell1_JRC_SS04956-20151125_20_B3-Aligned63xScale_c0.swc",]$match ="Cha-F-800096"
mf["cell1_GMR_37G11_AE_01-20140618_19_B3-Aligned63xScale_c0.swc",]$match ="Cha-F-800096"
mf["cell1_JRC_SS04956-20151125_20_B3-Aligned63xScale_c0.swc",]$match ="Cha-F-800096"
mf["cell2_JRC_SS04956-20151125_20_B1-Aligned63xScale_c0.swc",]$match ="Cha-F-800096"
# L2444; PN; AL-lALT-PN3
mf[c("GMR_MB583B-20121107_19_H4-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_MB583B-20121107_19_H4-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_MB583B-20121107_19_H4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "PN"
mf["JRC_SS44863-20180209_21_D6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-900038"
# L260; 143; PV1a; Good
mf[c("GMR_MB583B-20121107_19_H4-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_MB583B-20121107_19_H4-Aligned63xScale_c1.Smt5.SptGraph.swc",
"GMR_MB583B-20121107_19_H4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "143"
mf["GMR_MB583B-20121107_19_H4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="TH-M-000042"
mf["GMR_MB583B-20121107_19_H4-Aligned63xScale_c1.Smt5.SptGraph.swc",]$match ="TH-M-000042" # Duplicated
mf["GMR_MB583B-20121107_19_H4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="TH-M-000042" # Duplicated
# L16; 113 and mess; notLHproper
mf[c("GMR_SS00367-20180209_21_H5-Aligned63xScale_c2a.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H5-Aligned63xScale_c2b.Smt2.SptGraph.swc",
"GMR_SS00367-20131220_19_A4-Aligned63xScale_c2a.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H1-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "Input?" # Input type
mf[c("GMR_SS00367-20180209_21_H5-Aligned63xScale_c0a.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H5-Aligned63xScale_c0b.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H1-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS00367-20180209_21_H3-Aligned63xScale_c0.Smt.SptGraph.swc",
"GMR_SS00367-20131220_19_A4-Aligned63xScale_c1.Smt.SptGraph.swc",
"GMR_SS00367-20131220_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "113"
mf["GMR_SS00367-20180209_21_H5-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="fru-F-600136"
mf["GMR_SS00367-20180209_21_H5-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="PD2e2" #
mf["GMR_SS00367-20180209_21_H1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="PD2e2"
mf["GMR_SS00367-20180209_21_H3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-F-600136" # Duplicated
mf["GMR_SS00367-20131220_19_A4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="fru-F-600136"
mf["GMR_SS00367-20131220_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-F-600136" # Duplicated
mf["GMR_SS00367-20180209_21_H5-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="fru-M-200431"
mf["GMR_SS00367-20180209_21_H5-Aligned63xScale_c2b.Smt2.SptGraph.swc",]$match ="fru-M-200431"
mf["GMR_SS00367-20131220_19_A4-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="fru-M-200431"
mf["GMR_SS00367-20180209_21_H1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-M-200431"
# L173; 12B; PV5c1
mf[c("JRC_SS03225-20150828_24_F1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_G1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_G1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03225-20150828_24_G1-Aligned63xScale_c2a.Smt.SptGraph.swc"),]$old.cell.type = "12B"
mf["JRC_SS03225-20150828_24_F1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="E0585-F-300071"
mf["JRC_SS03225-20150828_24_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="E0585-F-300071" # Duplicated
mf["JRC_SS03225-20150828_24_F1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="E0585-F-300071" # Duplicated
mf["JRC_SS03225-20150828_24_F2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000317" # Duplicated
mf["JRC_SS03225-20150828_24_F2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000317"
mf["JRC_SS03225-20150828_24_F2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000317" # Duplicated
mf["JRC_SS03225-20150828_24_G1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-200232"
mf["JRC_SS03225-20150828_24_G1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200232"
mf["JRC_SS03225-20150828_24_G1-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="Gad1-F-200232"
# L1385; 1D; complicated
mf[c("JRC_SS04720-20170623_23_A4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c0b.Smt.SptGraph.swc"),]$old.cell.type = "1D"
mf["JRC_SS04720-20170623_23_A4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="130625c0"
mf["JRC_SS04720-20170623_23_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-000242"
mf["JRC_SS04720-20160819_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-000515" # Investigate further
mf["JRC_SS04720-20160819_21_C1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000515" # Investigate further
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="140618c0" # Investigate further
mf["JRC_SS04720-20160819_21_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-800100" # Investigate further
mf["JRC_SS04720-20170623_23_A2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-000515" # Duplicated Investigate further
mf["JRC_SS04720-20170623_23_A2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000515" # Investigate further
mf["JRC_SS04720-20170623_23_B1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Investigate further
mf["JRC_SS04720-20170623_23_A4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200366"
mf["JRC_SS04720-20170623_23_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-200366" # Duplicated
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Gad1-F-200127" # Investigate further
mf["JRC_SS04720-20160819_21_C3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-600241" # Close, could also be Gad1-F-700106
mf["JRC_SS04720-20170623_23_A7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-400436"
mf["JRC_SS04720-20170623_23_A7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-400436" # Duplicated
mf["JRC_SS04720-20170623_23_A8-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200366"
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Gad1-F-100077"
mf["JRC_SS04720-20160819_21_C2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-200385"
# L178; 12B; PV5c1
mf[c("JRC_SS04038-20170324_28_C5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04038-20170324_28_C5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04038-20170324_28_C5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04038-20170324_28_C7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "12B"
mf["JRC_SS04038-20170324_28_C5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="E0585-F-400025"
mf["JRC_SS04038-20170324_28_C5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="E0585-F-400025" # Duplicated
mf["JRC_SS04038-20170324_28_C5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="E0585-F-400025" # Duplicated
mf["JRC_SS04038-20170324_28_C7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="E0585-F-400025"
# L258; 54A; PV2a1
mf[c("JRC_SS04955-20151009_19_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B1-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B3-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B3-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04955-20151009_19_B5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54A"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B2-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS04955-20151009_19_B2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="131031c1"
mf["JRC_SS04955-20151009_19_B2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="131031c1"
mf["JRC_SS04955-20151009_19_B3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="5HT1A-M-100027"
mf["JRC_SS04955-20151009_19_B3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="5HT1A-M-100027" # Duplicated
mf["JRC_SS04955-20151009_19_B3-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="5HT1A-M-100027" # Duplicated
mf["JRC_SS04955-20151009_19_B3-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="5HT1A-F-100028" # Duplicated
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="5HT1A-M-100027"
mf["JRC_SS04955-20151009_19_B5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-300168"
# L421; 1B2; AV4c1
mf[c("JRC_SS04958-20160225_19_C1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C1-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C2-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C3-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04958-20160225_19_C3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "1B2"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="fru-F-500093"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="fru-F-500093"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="fru-F-400486"
mf["JRC_SS04958-20160225_19_C1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-F-500093" # Also 131003c1? sort out
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="fru-F-500093" # Also 131003c1? sort out
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="131003c1"
mf["JRC_SS04958-20160225_19_C3-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="131123c1"
mf["JRC_SS04958-20160225_19_C3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-F-400486"
# L1828; 29E & 8A;PV4b2 & AD3b1 (# Segmentation: L187; 29E; PV4b1)
mf[c("JRC_SS03773-20180209_21_A7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "29E"
mf[c("JRC_SS03773-20180209_21_A7-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "8A"
mf["JRC_SS03773-20180209_21_A7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000533"
mf["JRC_SS03773-20180209_21_A7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-400084"
# L509; 114A; PV4b2 (# Segmentation: not present)
mf[c("JRC_SS03773-20180209_21_A7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03783-20151231_33_A1-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "114A"
mf["JRC_SS03783-20151231_33_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="fru-M-200351"
mf["JRC_SS03783-20151231_33_A1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="fru-M-200351"
# L784; 4B; PV4a5/9
mf[c("JRC_SS03802-20180209_20_A3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03802-20180209_20_A5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS03802-20180209_20_A5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A" # What's up with all this?
mf["JRC_SS03802-20180209_20_A3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
# L1467; 4A; PV4a1:6/f1
mf[c("JRC_SS04967-20151022_20_A1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A2-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A3-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A7-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A8-Aligned63xScale_c3.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_B1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_B1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS04967-20151022_20_A1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="130703c0" # Check 130925c2? 130219c0? Cha-F-900046?
mf["JRC_SS04967-20151022_20_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-500234"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="130724c0"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="fru-F-400219"
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-F-400219" # Duplicated
mf["JRC_SS04967-20151022_20_A2-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="130911c2" # Check, Gad1-F-200395? 130724c0? VGlut-F-700430?
mf["JRC_SS04967-20151022_20_A3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="130625c0"
mf["JRC_SS04967-20151022_20_A3-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="fru-F-400219"
mf["JRC_SS04967-20151022_20_A5-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-400318" # Check, "Gad1-F-000381"?
mf["JRC_SS04967-20151022_20_A5-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Cha-F-500234" # check "130625c0"
mf["JRC_SS04967-20151022_20_A5-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="Cha-F-400318" # Check, "Gad1-F-000381"?
mf["JRC_SS04967-20151022_20_A5-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Gad1-F-000381" # Check, 130625c0? Cha-F-500234?
mf["JRC_SS04967-20151022_20_A7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-500253" # 130625c0 ? Cha-F-500234? 130411c2?
mf["JRC_SS04967-20151022_20_A7-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="Cha-F-500234"
mf["JRC_SS04967-20151022_20_A7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04967-20151022_20_A8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04967-20151022_20_A8-Aligned63xScale_c3.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04967-20151022_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="130704c1" # Check VGlut-F-500253?
mf["JRC_SS04967-20151022_20_B1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="fru-F-500479"
mf["JRC_SS04967-20151022_20_B1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="fru-F-500479" # Duplicated
mf["JRC_SS04967-20151022_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-F-500479" # Duplicated
mf["JRC_SS04967-20151022_20_A3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-600090"
# L1735; 4A; PV4a2/3/5
mf[c("JRC_SS04970-20150828_24_B1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04970-20150828_24_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04970-20150828_24_B1-Aligned63xScale_c3.Smt.SptGraph.swc",
"JRC_SS04970-20150828_24_B5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F7-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F7-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04970-20151002_21_F7-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS04970-20150828_24_B1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04970-20150828_24_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Cha-F-500234"
mf["JRC_SS04970-20150828_24_B1-Aligned63xScale_c3.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04970-20150828_24_B5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="130625c0"
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="130408c0"
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="130408c0" # Duplicated
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04970-20151002_21_F2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04970-20151002_21_F4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
mf["JRC_SS04970-20151002_21_F4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="130625c0"
mf["JRC_SS04970-20151002_21_F7-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="VGlut-F-500253" # Gad1-F-500281? 130408c0?
mf["JRC_SS04970-20151002_21_F7-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-100412"
mf["JRC_SS04970-20151002_21_F7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="VGlut-F-500253"
# L1475; 4A; PV4a2:4
mf[c("JRC_SS04974-20150828_24_H1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04974-20150828_24_H6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20151002_21_E1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04974-20151002_21_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04974-20151002_21_E1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04974-20151002_21_E2-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS04974-20150828_24_H1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000381" # 130411c2
mf["JRC_SS04974-20150828_24_H1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04974-20150828_24_H1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-000381" # 130703c0?
mf["JRC_SS04974-20150828_24_H3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-M-500368"
mf["JRC_SS04974-20150828_24_H3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="fru-M-500368" # Duplicated
mf["JRC_SS04974-20150828_24_H3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="fru-M-500368" # Duplicated, Gad1-F-000381?
mf["JRC_SS04974-20150828_24_H5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04974-20150828_24_H5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04974-20150828_24_H6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-000381"
mf["JRC_SS04974-20151002_21_E1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Unknown"
mf["JRC_SS04974-20151002_21_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Unknown"
mf["JRC_SS04974-20151002_21_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Unknown"
mf["JRC_SS04974-20151002_21_E2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "130703c0"
# L234; 4A; PV4a1/2
mf[c("JRC_SS15295-20151002_21_A5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15295-20151008_22_B5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15295-20151008_22_B5-Aligned63xScale_c0b.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS15295-20151002_21_A5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "130619c0"
mf["JRC_SS15295-20151008_22_B5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "fru-F-400219"
mf["JRC_SS15295-20151008_22_B5-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "fru-F-400219"
# L954; 4A; PV4a5
mf[c("JRC_SS16060-20151125_19_E7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16060-20151125_19_E7-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS16060-20151125_19_E7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-500253"
mf["JRC_SS16060-20151125_19_E7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-500253" # Duplicated
# L568; 54A + 1H; PV2a2 + AV4c1/b6
mf[c("JRC_SS16329-20151125_23_A6-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54A"
mf[c("JRC_SS16329-20151125_23_A1-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A6-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "1H"
# PV2a2
mf["JRC_SS16329-20151125_23_A6-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "5HT1A-M-100027"
mf["JRC_SS16329-20151125_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-000242"
# AV4c1/b6
mf["JRC_SS16329-20151125_23_A1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100051"
mf["JRC_SS16329-20151125_23_A1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "Cha-F-400293" # Not a great match...
mf["JRC_SS16329-20151125_23_A6-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "140213c1"
mf["JRC_SS16329-20151125_23_A6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-400293"
# L1473; 4A; PV4a1:4/7/9
mf[c("JRC_SS16345-20151022_20_D2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c1.Smt2.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D3-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D3-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D4-Aligned63xScale_c2.Smt3.SptGraph.swc",
"JRC_SS16345-20151022_20_D5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
mf["JRC_SS16345-20151022_20_D2-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "130205c2" # Check
mf["JRC_SS16345-20151022_20_D2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "130703c0" # Check
mf["JRC_SS16345-20151022_20_D2-Aligned63xScale_c1.Smt2.SptGraph.swc",]$match = "130625c0"
mf["JRC_SS16345-20151022_20_D2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "130411c2"
mf["JRC_SS16345-20151022_20_D3-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "fru-F-500479"
mf["JRC_SS16345-20151022_20_D3-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Cha-F-500234"
mf["JRC_SS16345-20151022_20_D3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "fru-F-400219"
mf["JRC_SS16345-20151022_20_D4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "130625c0"
mf["JRC_SS16345-20151022_20_D4-Aligned63xScale_c2.Smt3.SptGraph.swc",]$match = "130411c2"
mf["JRC_SS16345-20151022_20_D5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-700436" # Check
mf["JRC_SS16345-20151022_20_D5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "fru-F-400219"
mf["JRC_SS16345-20151022_20_D5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "fru-F-400219"
# L542; 4A; PV4a4
mf[c("JRC_SS16652-20170303_25_A2-Aligned63xScale_c0.Smt.SptGraph.swc",
"4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c0.swc",
"4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c1.swc",
"4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c2.swc"),]$old.cell.type = "4A"
mf["JRC_SS16652-20170303_25_A2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "130703c0"
mf["4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c0.swc",]$match ="Cha-F-500234"
mf["4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c1.swc",]$match ="fru-F-400219"
mf["4A_JRC_SS16652-20170303_25_A2-Aligned63xScale_c2.swc",]$match ="fru-F-400219"
# L1354; 4A; PV4a3
mf[c("JRC_SS22604-20160729_27_A2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22604-20160729_27_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"4A_JRC_SS22604-20160729_27_A2-Aligned63xScale_c0.swc",
"4A_JRC_SS22604-20160729_27_A2-Aligned63xScale_c1.swc"),]$old.cell.type = "4A"
mf["JRC_SS22604-20160729_27_A2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-000381"
mf["JRC_SS22604-20160729_27_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Gad1-F-000381"
mf["4A_JRC_SS22604-20160729_27_A2-Aligned63xScale_c0.swc",]$match ="VGlut-F-700436"
mf["4A_JRC_SS22604-20160729_27_A2-Aligned63xScale_c1.swc",]$match = "VGlut-F-600752"
# L2013; 54C; PV2a1
mf[c("JRC_SS23347-20170303_26_E2-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "54C"
mf["JRC_SS23347-20170303_26_E2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "131030c0" # not in line?
# L1539; 16B; AD1b1/b2/c1 (# Segmentation 16B; AD1b2)
mf[c("JRC_SS22647-20161007_29_E2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E6-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E6-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E7-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "16B"
mf[c("JRC_SS22647-20161007_29_E2-Aligned63xScale_c0b.Smt.SptGraph.swc"),]$old.cell.type = ""
mf["JRC_SS22647-20161007_29_E2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS22647-20161007_29_E3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS22647-20161007_29_E3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "120726c3"
mf["JRC_SS22647-20161007_29_E6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS22647-20161007_29_E6-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match = "130711c3"
mf["JRC_SS22647-20161007_29_E6-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "120913c1"
mf["JRC_SS22647-20161007_29_E7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120913c1"
mf["JRC_SS22647-20161007_29_E7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "120913c1"
mf["JRC_SS22647-20161007_29_E7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "130711c3"
mf["JRC_SS22647-20161007_29_E2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Gad1-F-200241"
# L1749; 116A & 4A; PD3a1/2/3 & PV4a7; (# Segmentation 116A; PD3a1)
mf[c("JRC_SS22723-20170324_29_F4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F5-Aligned63xScale_c1a.Smt3.SptGraph.swc",
"JRC_SS22723-20170324_29_F2-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "116A"
mf[c("JRC_SS22723-20170324_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F5-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "4A"
# PD3
mf["JRC_SS22723-20170324_29_F4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "PD3a4"
mf["JRC_SS22723-20170324_29_F5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "PD3a3"
mf["JRC_SS22723-20170324_29_F4-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "PD3a5"
mf["JRC_SS22723-20170324_29_F5-Aligned63xScale_c1a.Smt3.SptGraph.swc",]$match = "Cha-F-400165"
mf["JRC_SS22723-20170324_29_F2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200150"
# PV4a7
mf["JRC_SS22723-20170324_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F4-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
mf["JRC_SS22723-20170324_29_F5-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Gad1-F-100345"
# L1328; 138; PV2a1; Good
mf[c("JRC_SS16353-20170303_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16353-20170303_21_C6-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "138"
mf["JRC_SS16353-20170303_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-400222"
mf["JRC_SS16353-20170303_21_C2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-400222"
mf["JRC_SS16353-20170303_21_C5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-400222"
mf["JRC_SS16353-20170303_21_C5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-400222" # Duplicated
mf["JRC_SS16353-20170303_21_C6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-400222"
mf["JRC_SS16353-20170303_21_C6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-400222"
# L907; 27A; Av2a1; Good
mf[c("JRC_SS16364-20151217_22_B7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "27A1"
mf["JRC_SS16364-20151217_22_B7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-000240"
# L247; 1B; AV4a2/5
mf[c("JRC_SS16661-20151125_20_F1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16661-20151125_20_F1-Aligned63xScale_c2b.Smt.SptGraph.swc"),]$old.cell.type = "1B1"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-000481"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Cha-F-000481"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-000481"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "Cha-F-000481"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-000079"
mf["JRC_SS16661-20151125_20_F1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "Cha-F-600191"
# L1046; 1B; Av4a2/5/6
mf[c("JRC_SS16786-20151022_19_B3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B6-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B6-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B7-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B7-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16786-20151022_19_B7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "1B1"
mf["JRC_SS16786-20151022_19_B3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-400436" # Av4a5
mf["JRC_SS16786-20151022_19_B4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-000481" # Av4a5
mf["JRC_SS16786-20151022_19_B4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100051" # AV4b5
mf["JRC_SS16786-20151022_19_B6-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "fru-F-600131" # Av4a6
mf["JRC_SS16786-20151022_19_B6-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Gad1-F-700106" # Av4a2
mf["JRC_SS16786-20151022_19_B7-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "Cha-F-000481" # Av4a5
mf["JRC_SS16786-20151022_19_B7-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "fru-F-600131" # Av4a6
mf["JRC_SS16786-20151022_19_B7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-400436" # Av4a5
# L1827; 29E & others; PV4b1/2
mf[c("JRC_SS22732-20180209_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "29E" # Sure??
mf[c("JRC_SS22732-20180209_20_B1-Aligned63xScale_c2b.Smt.SptGraph.swc"),]$old.cell.type = "16F"
mf[c("JRC_SS22732-20180209_20_B2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B5-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B6-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B7-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B7-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "29E"
# PV6b1
mf["JRC_SS22732-20180209_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "PV6b1"
mf["JRC_SS22732-20180209_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "PV6b1"
# AD1d1
mf["JRC_SS22732-20180209_20_B1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "Gad1-F-300229"
# PV4b1/2
mf["JRC_SS22732-20180209_20_B2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "140117c2"
mf["JRC_SS22732-20180209_20_B4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "140117c2"
mf["JRC_SS22732-20180209_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B5-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B6-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "VGlut-F-400084" # Duplicated
mf["JRC_SS22732-20180209_20_B6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B7-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "VGlut-F-400084"
mf["JRC_SS22732-20180209_20_B7-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "140117c2"
# L629; 27A + 4A; AV2a1/2 + PV4a6 (# Segmentation AV2a1)
mf[c("JRC_SS22737-20160624_20_B3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B3-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B5-Aligned63xScale_c2b.Smt.SptGraph.swc"),]$old.cell.type = "27A"
mf[c("JRC_SS22737-20160624_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "4A"
# Av2
mf["JRC_SS22737-20160624_20_B3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B3-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-800214" # Duplicated
mf["JRC_SS22737-20160624_20_B4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-800214"
mf["JRC_SS22737-20160624_20_B5-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "fru-F-200126"
# PV4
mf["JRC_SS22737-20160624_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200395"
# L1842; 4G; PV4c2
mf[c("JRC_SS23341-20160805_24_A1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A5-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23341-20160805_24_A7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "4G"
mf["JRC_SS23341-20160805_24_A1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-100178"
mf["JRC_SS23341-20160805_24_A1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-100178" # Duplicated
mf["JRC_SS23341-20160805_24_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-100178" # Duplicated
mf["JRC_SS23341-20160805_24_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-400195"
mf["JRC_SS23341-20160805_24_A4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-400195"
mf["JRC_SS23341-20160805_24_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "VGlut-F-400195" # Duplicated
mf["JRC_SS23341-20160805_24_A5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-400195"
mf["JRC_SS23341-20160805_24_A7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "VGlut-F-400195"
# L1989; 17C; Av1a1; Good
mf[c("JRC_SS23827-20160902_22_A3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23827-20160902_22_A3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23827-20160902_22_A3-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23827-20160902_22_A4-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "17C"
mf["JRC_SS23827-20160902_22_A3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23827-20160902_22_A3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23827-20160902_22_A3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23827-20160902_22_A4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-500105"
# L1990; 17C; Av1a1
mf[c("JRC_SS23828-20160902_22_G1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS23828-20160902_22_G7-Aligned63xScale_c1b.Smt.SptGraph.swc"),]$old.cell.type = "17C"
mf["JRC_SS23828-20160902_22_G1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-200201" # Duplicated
mf["JRC_SS23828-20160902_22_G5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-200201"
mf["JRC_SS23828-20160902_22_G7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-200201" # Duplicated
mf["JRC_SS23828-20160902_22_G7-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "Cha-F-200201"
# L240; 1B; Av4a2/3/5
mf[c("JRC_SS10567-20151008_22_D1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D6-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D6-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS10567-20151008_22_D7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A1-Aligned63xScale_c0b.Smt2.SptGraph.swc",
"JRC_SS10567-20160408_21_A1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c1a.Smt2.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS10567-20160408_21_A4-Aligned63xScale_c0.Smt2.SptGraph.swc",
"JRC_SS10567-20160408_21_A4-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "1B1"
mf["JRC_SS10567-20151008_22_D1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-300146"
mf["JRC_SS10567-20151008_22_D1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20151008_22_D1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20151008_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20151008_22_D2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-400436"
mf["JRC_SS10567-20151008_22_D2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-400436"
mf["JRC_SS10567-20151008_22_D4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Cha-F-000481"
mf["JRC_SS10567-20151008_22_D4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000481"
mf["JRC_SS10567-20151008_22_D6-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20151008_22_D6-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-000524"
mf["JRC_SS10567-20151008_22_D7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-400436"
mf["JRC_SS10567-20151008_22_D7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Trh-M-500176"
mf["JRC_SS10567-20160408_21_A1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="Cha-F-600191"
mf["JRC_SS10567-20160408_21_A1-Aligned63xScale_c0b.Smt2.SptGraph.swc",]$match ="Cha-F-000481"
mf["JRC_SS10567-20160408_21_A1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-000481"
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c1a.Smt2.SptGraph.swc",]$match ="Gad1-F-000079" # Duplicated
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000079" # Duplicated
mf["JRC_SS10567-20160408_21_A4-Aligned63xScale_c0.Smt2.SptGraph.swc",]$match ="Gad1-F-000079"
mf["JRC_SS10567-20160408_21_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-000079"
# L374; 3E; PV5g1/2 (#Segmentation PV5g1)
mf[c("JRC_SS15112-20180209_20_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E1-Aligned63xScale_c1b.Smt2.SptGraph.swc",
"JRC_SS15112-20180209_20_E1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS15112-20180209_20_E7-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "3E"
mf["JRC_SS15112-20180209_20_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-200177"
mf["JRC_SS15112-20180209_20_E1-Aligned63xScale_c1b.Smt2.SptGraph.swc",]$match = "Gad1-F-200177"
mf["JRC_SS15112-20180209_20_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200177"
mf["JRC_SS15112-20180209_20_E2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-200177"
mf["JRC_SS15112-20180209_20_E2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200177" # Duplicated
mf["JRC_SS15112-20180209_20_E5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Gad1-F-300312"
mf["JRC_SS15112-20180209_20_E7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="Gad1-F-300312"
mf["JRC_SS15112-20180209_20_E7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Gad1-F-300312" # Duplicated
# L194; 116A; PD3a1 only
mf[c("JRC_SS15256-20151009_19_E1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "116A"
mf["JRC_SS15256-20151009_19_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-500011"
# L259; 54A; PV2a1
mf[c("JRC_SS15285-20150828_23_A1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS15285-20150828_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "54A"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "5HT1A-F-100028"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="Cha-F-300168"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="5HT1A-F-100028"
mf["JRC_SS15285-20150828_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "5HT1A-F-100028"
# L62; 12B 4? 29C; PV6a1
mf[c("JRC_SS15289-20160226_20_F2-Aligned63xScale_c0.Smt2.SptGraph.swc"),]$old.cell.type = "29C"
mf["JRC_SS15289-20160226_20_F2-Aligned63xScale_c0.Smt2.SptGraph.swc",]$match = "CL29CR_30H02"
# L1293; 12A; PV5c1
mf[c("JRC_SS16977-20150828_24_D4-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS16977-20150828_24_D4-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS16977-20150828_24_D4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20150828_24_E1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16977-20151002_21_G7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D3-Aligned63xScale_c3.Smt.SptGraph.swc",
"JRC_SS16977-20170623_22_D8-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "12A"
mf["JRC_SS16977-20150828_24_D4-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20150828_24_D4-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match = "130814c0" # Check, bad match, 130814c0? 130712c1? 130711c1?
mf["JRC_SS16977-20150828_24_D4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20150828_24_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20151002_21_G2-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20151002_21_G2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "E0585-F-400025"
mf["JRC_SS16977-20151002_21_G4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "130814c0"
mf["JRC_SS16977-20151002_21_G4-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "130814c0" # Duplicated
mf["JRC_SS16977-20151002_21_G4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "130814c0" # Duplicated
mf["JRC_SS16977-20151002_21_G7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-000317"
mf["JRC_SS16977-20151002_21_G7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "E0585-F-300071"
mf["JRC_SS16977-20170623_22_D1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "E0585-F-300071"
mf["JRC_SS16977-20170623_22_D1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "E0585-F-300071" # Duplicated
mf["JRC_SS16977-20170623_22_D3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "E0585-F-400008"
mf["JRC_SS16977-20170623_22_D3-Aligned63xScale_c3.Smt.SptGraph.swc",]$match = "E0585-F-400008"
mf["JRC_SS16977-20170623_22_D8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-000317"
# L1594; 101; Av4b1; Good
mf[c("JRC_SS16986-20180209_21_B3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16986-20180209_21_B3-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "101"
mf["JRC_SS16986-20180209_21_B3-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-800067"
mf["JRC_SS16986-20180209_21_B3-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-800067" # Duplicated
# L2278; 16B; AD1b2
mf[c("JRC_SS24645-20161007_28_B3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B6-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS24645-20161007_28_B7-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "16B"
mf["JRC_SS24645-20161007_28_B3-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS24645-20161007_28_B4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS24645-20161007_28_B6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS24645-20161007_28_B7-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "120714c4"
mf["JRC_SS24645-20161007_28_B7-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "120714c4" # Duplicated
mf["JRC_SS24645-20161007_28_B7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "120714c4" # Duplicated
# L2385; 116B; PD3a2
mf[c("JRC_SS24840-20160909_25_F1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS24840-20160909_25_F1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "116B"
mf["JRC_SS24840-20160909_25_F1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Gad1-F-200150"
mf["JRC_SS24840-20160909_25_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Gad1-F-200150"
# L876; 116A + 27A; PD3a1/2 + Av2a2/e1
mf[c("JRC_SS25832-20170324_29_D5-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_D5-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_D5-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_E1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_E1-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "27A1"
mf[c("JRC_SS25832-20170324_29_D5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS25832-20170324_29_E1-Aligned63xScale_c2.Smt.SptGraph.swc"),]$old.cell.type = "116A"
mf["JRC_SS25832-20170324_29_D5-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match = "Cha-F-500105"
mf["JRC_SS25832-20170324_29_D5-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match = "Cha-F-500105"
mf["JRC_SS25832-20170324_29_D5-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match = "Cha-F-500105"
mf["JRC_SS25832-20170324_29_E1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "Cha-F-500105"
mf["JRC_SS25832-20170324_29_E1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "Cha-F-500105" # Duplicated
# PD3a
mf["JRC_SS25832-20170324_29_D5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Gad1-F-200150"
mf["JRC_SS25832-20170324_29_E1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "Cha-F-400165"
# L1479; 1H; AV4a1
mf[c("JRC_SS04973-20151125_23_E4-Aligned63xScale_c0.Smt.SptGraph.swc"),]$old.cell.type = "1H"
mf["JRC_SS04973-20151125_23_E4-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="fru-M-700211"
# L979; 29D + others; PV4d3/4 (+ PV1a1 - in image?)
mf[c("JRC_SS04972-20180209_21_F8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F8-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F8-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F5-Aligned63xScale_c2b.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04972-20180209_21_F5-Aligned63xScale_c1.Smt.SptGraph.swc"),]$old.cell.type = "29D"
mf["JRC_SS04972-20180209_21_F8-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-600209"
mf["JRC_SS04972-20180209_21_F8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-600209"
mf["JRC_SS04972-20180209_21_F8-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="130912c1"
mf["JRC_SS04972-20180209_21_F8-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="130912c1"
mf["JRC_SS04972-20180209_21_F5-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="Cha-F-600209"
mf["JRC_SS04972-20180209_21_F5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="Cha-F-600209"
mf["JRC_SS04972-20180209_21_F5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="Cha-F-600209"
# Not LH proper
mf["JRC_SS15112-20180209_20_E1-Aligned63xScale_c0.Smt.SptGraph.swc",]$match = "notLHproper"#"Trh-M-100087"
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS04720-20160819_21_C7-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS04720-20170623_23_A2-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS10567-20151008_22_D6-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS15112-20180209_20_E5-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS16786-20151022_19_B3-Aligned63xScale_c0a.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS16786-20151022_19_B3-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS16786-20151022_19_B6-Aligned63xScale_c0b.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS16786-20151022_19_B6-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS23347-20170303_26_E2-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS23347-20170303_26_E2-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS24820-20161007_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",]$match ="notLHproper"
mf["JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="notLHproper"
# Mis-registered
mf["JRC_SS03802-20180209_20_A8-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS03802-20180209_20_A8-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS03802-20180209_20_A8-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS04958-20160225_19_C2-Aligned63xScale_c2a.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS04967-20151022_20_A1-Aligned63xScale_c1b.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS04967-20151022_20_A1-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS04967-20151022_20_A3-Aligned63xScale_c1a.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS22723-20170324_29_F5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS03225-20150828_24_G1-Aligned63xScale_c2b.Smt.SptGraph.swc",]$match = "mis-registered" # Or "131204c0"
mf["JRC_SS03802-20180209_20_A5-Aligned63xScale_c1.Smt.SptGraph.swc",]$match = "mis-registered" #"130205c2"
mf["JRC_SS03802-20180209_20_A5-Aligned63xScale_c2.Smt.SptGraph.swc",]$match = "mis-registered" #"130205c2" # Duplicated
# Badly traced
mf["JRC_SS22732-20180209_20_B7-Aligned63xScale_c2.Smt.SptGraph.swc",]$match ="mis-registered"
mf["JRC_SS16329-20151125_23_A6-Aligned63xScale_c0.Smt.SptGraph.swc",]$match ="mis-registered" # 1H
###################
# Make New Matches #
###################
# If for MCFO skeleton is not, for some reason, in most.lhns
df.a = most.lhns.old[,c("pnt","anatomy.group","cell.type","type")]
df.b = data.frame(pnt = most.lhins.old[,c("tract")],anatomy.group=most.lhins.old[,c("anatomy.group")],cell.type=most.lhins.old[,c("anatomy.group")], type = "IN")
rownames(df.b) = names(most.lhins.old)
df = rbind(df.b,df.a[!rownames(df.a)%in%rownames(df.b),])
mf$pnt = as.character(sapply(mf$match,function(x) df[x,]$pnt))
mf$anatomy.group = as.character(sapply(mf$match,function(x) df[x,]$anatomy.group))
mf$cell.type = as.character(sapply(mf$match,function(x) df[x,]$cell.type))
mf$type = as.character(sapply(mf$match,function(x) df[x,]$type))
#################
# New cell types #
#################
mf[grepl("PV6b1",mf$match),]$pnt = "PV6"
mf[grepl("PV6b1",mf$match),]$anatomy.group = "PV6b"
mf[grepl("PV6b1",mf$match),]$type = "ON"
mf[grepl("PV6b1",mf$match),]$cell.type = "PV6b1"
mf[grepl("PD3a3",mf$match),]$pnt = "PD3"
mf[grepl("PD3a3",mf$match),]$anatomy.group = "PD3a"
mf[grepl("PD3a3",mf$match),]$type = "LN"
mf[grepl("PD3a3",mf$match),]$cell.type = "PD3a3"
mf[grepl("PD3a4",mf$match),]$pnt = "PD3"
mf[grepl("PD3a4",mf$match),]$anatomy.group = "PD3a"
mf[grepl("PD3a4",mf$match),]$type = "LN"
mf[grepl("PD3a4",mf$match),]$cell.type = "PD3a4"
mf[grepl("PD3a5",mf$match),]$pnt = "PD3"
mf[grepl("PD3a5",mf$match),]$anatomy.group = "PD3a"
mf[grepl("PD3a5",mf$match),]$type = "LN"
mf[grepl("PD3a5",mf$match),]$cell.type = "PD3a5"
mf[grepl("PD2e2",mf$match),]$pnt = "PD2"
mf[grepl("PD2e2",mf$match),]$anatomy.group = "PD2e"
mf[grepl("PD2e2",mf$match),]$type = "ON"
mf[grepl("PD2e2",mf$match),]$cell.type = "PD2e2"
mf[grepl("AV6c1",mf$match),]$pnt = "AV6"
mf[grepl("AV6c1",mf$match),]$anatomy.group = "AV6c"
mf[grepl("AV6c1",mf$match),]$type = "ON"
mf[grepl("AV6c1",mf$match),]$cell.type = "AV6c1"
mf[grepl("PV6a3",mf$match),]$pnt = "PV6"
mf[grepl("PV6a3",mf$match),]$anatomy.group = "PV6a"
mf[grepl("PV6a3",mf$match),]$type = "ON"
mf[grepl("PV6a3",mf$match),]$cell.type = "PV6a3"
mf[grepl("AV4f1",mf$match),]$pnt = "AV4"
mf[grepl("AV4f1",mf$match),]$anatomy.group = "AV4f"
mf[grepl("AV4f1",mf$match),]$type = "ON"
mf[grepl("AV4f1",mf$match),]$cell.type = "AV4f1"
mf[grepl("PV6c1",mf$match),]$pnt = "PV6"
mf[grepl("PV6c1",mf$match),]$anatomy.group = "PV6c"
mf[grepl("PV6c1",mf$match),]$type = "ON"
mf[grepl("PV6c1",mf$match),]$cell.type = "PV6c1"
mf[grepl("WED-PN3",mf$match),]$pnt = "WEDT"
mf[grepl("WED-PN3",mf$match),]$anatomy.group = "WED-PN"
mf[grepl("WED-PN3",mf$match),]$type = "IN"
mf[grepl("WED-PN3",mf$match),]$cell.type = "WED-PN3"
mf[grepl("WED-PN5",mf$match),]$pnt = "WEDT"
mf[grepl("WED-PN5",mf$match),]$anatomy.group = "WED-PN"
mf[grepl("WED-PN5",mf$match),]$type = "IN"
mf[grepl("WED-PN5",mf$match),]$cell.type = "WED-PN5"
mf[grepl("AD1d1",mf$match),]$pnt = "AD1"
mf[grepl("AD1d1",mf$match),]$anatomy.group = "AD1d"
mf[grepl("AD1d1",mf$match),]$type = "ON"
mf[grepl("AD1d1",mf$match),]$cell.type = "AD1d1"
mf[grepl("MB-C1",mf$match),]$pnt = "PV2"
mf[grepl("MB-C1",mf$match),]$anatomy.group = "MB-LH"
mf[grepl("MB-C1",mf$match),]$type = "ON"
mf[grepl("MB-C1",mf$match),]$cell.type = "MB-C1"
###################################################
# Mike Dolan determines what is in exemplar lines #
###################################################
mf[,"InLine"] = TRUE
mf[c("JRC_SS22723-20170324_29_F2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22723-20170324_29_F5-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C1-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C3-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A2-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_B1-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C3-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS04720-20170623_23_A8-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS04720-20160819_21_C2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS04967-20151022_20_A5-Aligned63xScale_c2a.Smt.SptGraph.swc",
"JRC_SS23347-20170303_26_E2-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C4-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS03773-20180209_21_A7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B6-Aligned63xScale_c2.Smt2.SptGraph.swc",
"JRC_SS21811-20161007_29_B7-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS21811-20161007_29_B8-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C4-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS16351-20160819_23_C6-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B1-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS22732-20180209_20_B1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS03773-20180209_21_A7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A6-Aligned63xScale_c1a.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS24820-20161007_29_F1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS25950-20161104_19_A4-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16564-20160311_23_D7-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22730-20160701_22_E1-Aligned63xScale_c1.Smt.SptGraph.swc",
"JRC_SS22730-20160701_22_E7-Aligned63xScale_c0.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A1-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS16329-20151125_23_A6-Aligned63xScale_c1b.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c0b.Smt.SptGraph.swc",
"JRC_SS16345-20151022_20_D2-Aligned63xScale_c0a.Smt.SptGraph.swc",
"JRC_SS22737-20160624_20_B5-Aligned63xScale_c2.Smt.SptGraph.swc",
"JRC_SS22647-20161007_29_E3-Aligned63xScale_c1.Smt.SptGraph.swc"
),"InLine"] = FALSE
#############
# Save data #
#############
mf$neurotransmitter = as.character(sapply(mf[,"old.cell.type"],function(x) subset(stainings,old.cell.type==x)$NT[1]))
mf$cell.number = as.character(sapply(mf[,"old.cell.type"],function(x) subset(stainings,old.cell.type==x)$no.cells[1]))
mf$coreLH = FALSE
lh.mcfo = mcfo
order = order(mf$linecode)
mf = mf[order,]
lh.mcfo = lh.mcfo[order]
r <- rle(as.character(mf$linecode))
rownames(mf) = names(lh.mcfo) = paste0(rep(r$values, times = r$lengths), "#",unlist(lapply(r$lengths, seq_len)))
mf = mf[,-3]
attr(lh.mcfo,"df") = mf
################
# Make Matches #
################
# Synchronise with most.lhns
most.lh = nat::union(most.lhns.old,most.lhins.old)
in.most.lhns = names(lh.mcfo)[names(lh.mcfo)%in%names(most.lh)]
lh.mcfo[in.most.lhns,c("pnt","anatomy.group","cell.type","type","coreLH")] = most.lh[in.most.lhns,c("pnt","anatomy.group","cell.type","type","coreLH")]
lh.mcfo[,"id"] = names(lh.mcfo)
# remove non=ASCII chracter
lh.mcfo[,] = change_nonascii(lh.mcfo[,])
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