can I donwload the anatomical masks

[bys...@gmail.com]

Dear VirtualFlyBrain,

I'm a PhD student at FMI in Basel. I'm now trying to plot a 3D compartamental model of the mushroom body. For example, plot the PAM and PPL neurons as color-coded clusters.

Is it possible for me to download those anatomical masks? 

Thank you very mush.

Best,

Wenbin

[Marta Costa]

Dear Wenbin,

The mask with the original labeled anatomical domains for JFRC2 (Ito et al., 2014), including the ones for the mushroom body is linked from here https://www.virtualflybrain.org/site/vfb_site/template_files_downloads.htm

It includes:

"MB_PED_R" "MB_VL_R"  "MB_ML_R"  "MB_CA_R"  "MB_PED_L" "MB_VL_L"  "MB_ML_L"  "MB_CA_L” 

These volumes are available to plot directly using the R package nat.flybrains, developed by Greg Jefferis and his group.

http://natverse.org/nat.flybrains/

If you are using the JFRC2 template, you’d use the the JFRC2NP.surf object. The volumes have also been bridged to other public template brains, and those are also available in the package. Please see the examples in the link above.

Best wishes,

Marta Costa 

--

Marta Costa, PhD

Senior Research Associate

Virtual Fly Brain project

Department of Zoology

University of Cambridge,

Downing Street

Cambridge, CB2 3EJ, UK

mm...@cam.ac.uk

Twitter: @martamcosta2

http://www.virtualflybrain.org

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[Marta Costa]

Dear Wenbin,

Just to add that if you use python and not R, you can use the package pymaid (developed by Philipp Schlegel) to fetch the volumes from the nat.flybrains package.

https://pymaid.readthedocs.io/en/latest/index.html 

https://pymaid.readthedocs.io/en/latest/source/rmaid_doc.html (for specific install requirements for rmaid)

from pymaid import rmaid# Get the whole FCWB surface model
fcwb = rmaid.get_brain_volume('FCWB.surf')# Get e.g. the LH
fcwb_lh = rmaid.get_brain_volume('FCWBNP.surf', neuropil='LH_R')

Best wishes,

Marta

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