JFRC2NP.surf: Surface model of the Insect Brain Name Working Group neuropil...

In jefferislab/nat.flybrains: Additional data for use with the NeuroAnatomy Toolbox (nat)

Surface model of the Insect Brain Name Working Group neuropil segmentation in JFRC2 coordinate space

Description

Surface model of the Insect Brain Name Working Group neuropil segmentation in JFRC2 coordinate space

Details

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

References

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

See Also

JFRC2

Examples

# 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)

jefferislab/nat.flybrains documentation built on Aug. 16, 2022, 8:54 p.m.