can I donwload the anatomical masks

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bys...@gmail.com

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Jan 10, 2020, 9:23:48 AM1/10/20
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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

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Jan 10, 2020, 11:22:18 AM1/10/20
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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.

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
Twitter: @martamcosta2


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Marta Costa

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Jan 10, 2020, 12:30:10 PM1/10/20
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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/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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