Script to generate Allen mouse brain atlas with barrel annotations

[abisi]

Hello!

I added a script to generate a new BrainGlobe Atlas object that is the Allen Mouse Brain atlas using barrel annotations derived from work at the Blue Brain Project, EPFL. The resolutions are either 10 or 25 microns. Github repo for barrel annotations: https://github.com/BlueBrain/atlas-enhancement/tree/main/barrel-annotations Preprint: https://www.biorxiv.org/content/10.1101/2023.08.24.554204v2

These annotations refine the SSp-bfd structure with additional children which are the barrel columns, themselves containing children for each cortical layers. The end goal in my case is to more accurately track Neuropixels probe location within the SSp-bfd region. However these annotations may be useful for a larger community as well as for other applications.

To add these annotations, I used pregenerated annotations volumes in lieu of the current annotations, shared by the author of the code @alTeska. I have manually added the structures in the hierarchy as the .json files were organized differently (dict of dicts in BlueBrain code, vs. list of dicts in Allen structures.json). In particular I retained the original SSp-bfd cortical layers (1-2/3-4-5-6a-6b) as children of SSp-bfd. Then I added the columns e.g. SSp-bfd-A1 and their children for cortical layers e.g. SSp-bfd-A1-1, etc. Note: the BlueBrain hierarchy contains layers 2 and 3 as children of 2/3. For clarity and ease of use I have unilaterally decided to exclude the former, as often layers 2/3 are analyzed jointly. 😄

Because these pregenerated files are not hosted online, I need to share them with you so you may test. Can you access this link? https://drive.google.com/drive/folders/1xVEEdhZIYKsDNDimiPO850Pwz4ZCdsg2?usp=sharing

I guess ultimately it'd be cleaner to use the above-mentioned code to regenerate these files from scratch? This would require using the transplant_barrels.nrrd.py script (https://github.com/BlueBrain/atlas-enhancement/blob/main/barrel-annotations/transplant_barrels_nrrd.py).

Let me know if there are any issues or questions! Thank you for your help!

Axel

[alessandrofelder]

Thank @abisi - I'll have a look next week!

[alessandrofelder]

Thanks a lot @abisi - this is looking good. With some minor hacks, I managed to reproduce a nice-looking barrel-enhanced BrainGlobe atlas :tada:

I've done an initial top-level review for now, just some things I've noticed - I hope it's helpful :smiley: feel free to ask for clarification on my comments, and to disagree with them as much as you like! You can post them either as responses here, or message us on zulip. My only major worry is how to install atlas-enhancement cleanly but maybe you can help?

Am I right in thinking your script currently doesn't create meshes for the new regions you introduce? You should be able to do this with our helper function create_region_mesh (see e.g. https://github.com/brainglobe/brainglobe-atlasapi/blob/6a4f7ab5a109ded62704c99607f4905c3aec5b18/brainglobe_atlasapi/atlas_generation/atlas_scripts/cavefish_atlas.py#L128C1-L151C14)

I have manually added the structures in the hierarchy as the .json files were organized differently (dict of dicts in BlueBrain code, vs. list of dicts in Allen structures.json).

Just to double-check, what do you mean by manually here. It looks to me like you've done this programmatically from your code, which I think is more than reasonable?

Can you access this link? drive.google.com/drive/folders/1xVEEdhZIYKsDNDimiPO850Pwz4ZCdsg2?usp=sharing

I have access now, thanks to @alTeska :pray:

[alessandrofelder]

Just a quick additional note that I've run the atlas through the validation script (a modified local version of the checks implemented in validate_atlases.py), so validation runs just on one atlas.

Validation passes up to some missing meshes, which presumably links to my comment above that we should add meshes for the new regions. Out of curiosity, how did you choose the barrel-related ID numbers?

Validation failure details

```bash Structures with IDs [545, 614454385, 614454386, 614454389, 614454390, 614454391, 614454392, 614454384, 614454394, 614454395, 614454398, 614454399, 614454400, 614454401, 614454393, 614454403, 614454404, 614454407, 614454408, 614454409, 614454410, 614454402, 614454412, 614454413, 614454416, 614454417, 614454418, 614454419, 614454411, 614454421, 614454422, 614454425, 614454426, 614454427, 614454428, 614454420, 614454430, 614454431, 614454434, 614454435, 614454436, 614454437, 614454429, 614454439, 614454440, 614454443, 614454444, 614454445, 614454446, 614454438, 614454448, 614454449, 614454452, 614454453, 614454454, 614454455, 614454447, 614454457, 614454458, 614454461, 614454462, 614454463, 614454464, 614454456, 614454466, 614454467, 614454470, 614454471, 614454472, 614454473, 614454465, 614454475, 614454476, 614454479, 614454480, 614454481, 614454482, 614454474, 614454484, 614454485, 614454488, 614454489, 614454490, 614454491, 614454483, 614454493, 614454494, 614454497, 614454498, 614454499, 614454500, 614454492, 614454502, 614454503, 614454506, 614454507, 614454508, 614454509, 614454501, 614454511, 614454512, 614454515, 614454516, 614454517, 614454518, 614454510, 614454520, 614454521, 614454524, 614454525, 614454526, 614454527, 614454519, 614454529, 614454530, 614454533, 614454534, 614454535, 614454536, 614454528, 614454538, 614454539, 614454542, 614454543, 614454544, 614454545, 614454537, 614454547, 614454548, 614454551, 614454552, 614454553, 614454554, 614454546, 614454556, 614454557, 614454560, 614454561, 614454562, 614454563, 614454555, 614454565, 614454566, 614454569, 614454570, 614454571, 614454572, 614454564, 614454574, 614454575, 614454578, 614454579, 614454580, 614454581, 614454573, 614454583, 614454584, 614454587, 614454588, 614454589, 614454590, 614454582, 614454592, 614454593, 614454596, 614454597, 614454598, 614454599, 614454591, 614454601, 614454602, 614454605, 614454606, 614454607, 614454608, 614454600, 614454610, 614454611, 614454614, 614454615, 614454616, 614454617, 614454609, 614454619, 614454620, 614454623, 614454624, 614454625, 614454626, 614454618, 614454628, 614454629, 614454632, 614454633, 614454634, 614454635, 614454627, 614454637, 614454638, 614454641, 614454642, 614454643, 614454644, 614454636, 614454646, 614454647, 614454650, 614454651, 614454652, 614454653, 614454645, 614454655, 614454656, 614454659, 614454660, 614454661, 614454662, 614454654, 614454664, 614454665, 614454668, 614454669, 614454670, 614454671, 614454663, 614454673, 614454674, 614454677, 614454678, 614454679, 614454680, 614454672] are in the atlas, but don't have a corresponding mesh file. ```

(The fact that region 545 is missing is a known issue, I think the other ID are barrel-related)

[abisi]

Hello,

Great, thank you for looking into this so quickly! I am at a conference all week so I may only update you middle of next week!

Axel