In natverse/fafbseg: Support Functions for Analysis of FAFB EM Segmentation

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
rgl::setupKnitr()
havelmr=require('elmr', quietly = TRUE)
options(nat.plotengine = 'plotly')

Introduction

This articles gives a quick overview of mapping points between FAFB14 (as used by the "walled garden" and Virtual Fly Brain and FlyWire.

library(fafbseg)

Basic point mapping

Some known points

# identified location in FAFB14
p.fafb.nm <- cbind(477042, 284535, 90680)
p.fafb.raw <- p.fafb.nm/c(4,4,40)
# corresponding location in FlyWire
p.flywire.raw <- cbind(118865, 71338, 2267)
p.flywire.nm <- p.flywire.raw * c(4,4,40)

Compare displacements (in nm) for forward or inverse mapping

# check displacement
flywire2fafb(p.flywire.nm)-p.fafb.nm

# check what happens when you apply the inverse
fafb2flywire(p.fafb.nm)-p.flywire.nm

A sample neuron. First map the points

data("AV4b1", package='catmaid')
before=xyzmatrix(AV4b1)
after=fafb2flywire(before)

Then some stats and a quick histogram

d=sqrt(rowSums((before-after)^2))
summary(d)

hist(d, br=20, main='Displacement /µm')

sample_points_in_surf <- function(x, n){
  x=as.mesh3d(x)
  bb=boundingbox(x)
  mm=mapply(runif, min=bb[1,], max=bb[2,], n = n)
  colnames(mm)=c("X","Y","Z")
  data.frame(mm, inside=pointsinside(mm,x))
}

set.seed(42)
sxyz=sample_points_in_surf(FAFB14.surf,25000)
sxyz.in=subset(sxyz, inside)
sxyz.fw=fafb2flywire(xyzmatrix(sxyz.in))
deltas=sxyz.fw-sxyz.in
delta=rowSums(deltas[,c("X","Y")])

jet.colors<-colorRampPalette(c('navy','cyan','yellow','red'))
nclear3d();
spheres3d(xyzmatrix(sxyz.in), col=jet.colors(10)[cut(delta, breaks = 10)], rad=2000)

Round trip error

Let's send those points back again

sxyz.fafb2=flywire2fafb(sxyz.fw)

deltas=sxyz.fafb2-xyzmatrix(sxyz.in)
delta=rowSums(deltas[,c("X","Y")])
hist(delta, main = "Round Trip Error", xlab='delta /nm')

Mapping anything

To map complex objects, use xform_brain()

AV4b1.fw=xform_brain(AV4b1, sample='FAFB14', reference = 'FlyWire')

# find the main branch point of a neuron, a good place to point to
mainbranch <- function(x, ...) {
  if(is.neuronlist(x)) 
    return(nlapply(x, mainbranch, ...))

  sx=nat::simplify_neuron(x, ...)
  xyzmatrix(sx)[sx$BranchPoints,]
}

choose_segmentation("flywire")
open_fafb_ngl(mainbranch(AV4b1.fw), coords.only = TRUE)

{width=400px} {width=800px}

Note the relevant links:

catmaid.url="https://garden.catmaid.org/tracing/fafb/v14/?pid=1&zp=146720&yp=162452&xp=353219&tool=tracingtool&active_skeleton_id=488055&active_node_id=2693476&sid0=5&s0=1"

fwurl="https://ngl.flywire.ai/#!%7B%22layers%22:%5B%7B%22source%22:%22precomputed://gs://microns-seunglab/drosophila_v0/alignment/image_rechunked%22%2C%22type%22:%22image%22%2C%22blend%22:%22default%22%2C%22shaderControls%22:%7B%7D%2C%22name%22:%22Production-image%22%7D%2C%7B%22source%22:%22graphene://https://prodv1.flywire-daf.com/segmentation/1.0/fly_v31%22%2C%22type%22:%22segmentation_with_graph%22%2C%22segments%22:%5B%220%22%2C%22720575940618054533%22%5D%2C%22skeletonRendering%22:%7B%22mode2d%22:%22lines_and_points%22%2C%22mode3d%22:%22lines%22%7D%2C%22graphOperationMarker%22:%5B%7B%22annotations%22:%5B%5D%2C%22tags%22:%5B%5D%7D%2C%7B%22annotations%22:%5B%5D%2C%22tags%22:%5B%5D%7D%5D%2C%22pathFinder%22:%7B%22color%22:%22#ffff00%22%2C%22pathObject%22:%7B%22annotationPath%22:%7B%22annotations%22:%5B%5D%2C%22tags%22:%5B%5D%7D%2C%22hasPath%22:false%7D%7D%2C%22name%22:%22Production-segmentation_with_graph%22%7D%5D%2C%22navigation%22:%7B%22pose%22:%7B%22position%22:%7B%22voxelSize%22:%5B4%2C4%2C40%5D%2C%22voxelCoordinates%22:%5B88371.25%2C40478.75%2C3668%5D%7D%7D%2C%22zoomFactor%22:8%7D%2C%22perspectiveZoom%22:2230.6094%2C%22jsonStateServer%22:%22https://globalv1.flywire-daf.com/nglstate/post%22%2C%22selectedLayer%22:%7B%22layer%22:%22Production-segmentation_with_graph%22%2C%22visible%22:true%7D%2C%22layout%22:%22xy-3d%22%7D"

Load the flywire mesh

av4.fwm=read_cloudvolume_meshes('720575940618054533')

And plot with the CATMAID skeleton

nclear3d()
plot3d(AV4b1.fw, col='red', lwd=3)
wire3d(av4.fwm[[1]], col='grey', alpha=.2)

It's obvious that both are only partially traced, but they are still the same neuron.

natverse/fafbseg documentation built on Nov. 11, 2024, 9:50 p.m.