ROIs coordinates

Letícia Batista

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Feb 14, 2022, 5:49:05 AM2/14/22

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Hi all,

I'm trying to define the cell position of some antennal lobe neurons in respect to the AL itself. For that, would be very cool to have the AL ROI coordinates (x,y,z) to automate the process. Do you know where I can get such information about the ROIs? Either on the website or on the R natverse packages would be great!

Thanks a lot!

Stuart Berg

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Feb 14, 2022, 9:58:05 AM2/14/22

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Hi Letícia,

You can download the ROI compartment masks as a low-resolution hdf5 volume. See this thread for details:

https://groups.google.com/g/neuprint/c/2jAfAHW6tkc/m/J4nkFVTNAAAJ

(The hemibrain ROI shapes have not changed since our v1.1 release.)

Best,

Stuart

Greg Jefferis

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Feb 14, 2022, 11:28:31 AM2/14/22

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Dear Letícia,

Just to note that thread Stuart mentions provides a good way to map arbitrary XYZ locations to their neuropil identity including the antennal lobe glomeruli which may be what you are interested in. However you may also like to get the surface mesh representations of those structures. You can do this on the R / natverse side using the hemibrainr package.

See for example

https://natverse.org/hemibrainr/articles/meta_data.html

There are actually three sets of glomerulus surfaces: one that you can fetch from the neuprint server (using hemibrain_roi_meshes()) and two distributed with the hemibrainr package (see hemibrain_al.surf) based on analysis of ORNs or PNs, respectively. Slightly unfortunately these glomerulus surfaces are not identical but there were good reasons for this (see Schlegel, Bates et al eLife 2021 for the full details)