JFRC2NP.surf | R Documentation |
Surface model of the Insect Brain Name Working Group neuropil segmentation in JFRC2 coordinate space
Note that the supplementary information for the Insect Brain Name
working group only includes neuropil information in the IBN
space, which can be downloaded from
ftp://flybase.org/flybase/associated_files/InsectBrainNomenclature_RawData.zip.
However Arnim Jenett, Kazunori Shinomiya and Kei Ito generated a full brain
segmentation based on the JFRC2
template (used by the Virtual
Fly Brain project and internally at Janelia Farm for several years.)
This surface model was generated in Amira from the segmentation in the file
JFRCtempate2010.mask130819.am
with md5
d0a40b38d1a0045a423d947ebf1778d2
. The data are available in a github
repository https://github.com/VirtualFlyBrain/DrosAdultBRAINdomains.
The original full size model was then simplified to reduce the number of
vertices resulting
Kei Ito, Kazunori Shinomiya, Masayoshi Ito, J. Douglas Armstrong, George Boyan, Volker Hartenstein, Steffen Harzsch, Martin Heisenberg, Uwe Homberg, Arnim Jenett, Haig Keshishian, Linda L. Restifo, Wolfgang Rössler, Julie H. Simpson, Nicholas J. Strausfeld, Roland Strauss, Leslie B. Vosshall, Insect Brain Name Working Group (2013). A systematic nomenclature for the insect brain. Neuron 81 (4), 755-765. doi:10.1016/j.neuron.2013.12.017
JFRC2
# list the materials for the different surface regions materials(JFRC2NP.surf) ## Not run: # plot the surface plot3d(JFRC2NP.surf) # calculate volumes ond surface areas for all regions if(require("RvtkStatismo") && require("tidyr") && require("ggplot2") && require("stringr")){ # convert each region to a mesh3d object, note that we use simplify=FALSE # to stop sapply mangling the result meshes=sapply(JFRC2NP.surf$RegionList, function(r) as.mesh3d(subset(JFRC2NP.surf, r)), simplify=FALSE) # now calculate information for each mesh # NB vtkMeshInfo returns a list so we need to convert to a vector # to end up with a nice matrix output vs=sapply(meshes, function(x) unlist(vtkMeshInfo(x))) # now make that into a tidy data.frame and plot df=data.frame(key=colnames(vs), t(vs), region=sub("_[LR]", "", colnames(vs)), side=str_match(colnames(vs), "_([LR])")[,2]) df2=gather(df, measure, value, volume:surfaceArea) library(ggplot2) qplot( value, region, data=df2, col=side, facets = . ~ measure) + scale_x_log10() } ## End(Not run)
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