[Feature] How to print all "nicknames" for brain regions in a given atlas?

[Eddymorphling]

Hi all, I am new to brainrender and I have a very simple yet naive q. How do I identify all the "nicknames" for all the brain regions for a given atlas? For example :

scene = Scene(atlas_name="perens_lsfm_mouse_20um", inset=False, title='3D_Brain')

# Get the brain region (Cortex, for example)
region1= scene.add_brain_region("SSp-ll4",  alpha=0.9)
```)

Here SSp-II4 is a one region. I would like to add more regions. What should I pass to print all brains regions and their "nicknames" (SSp-II4) in the perens mouse atlas for example? Could not find this in the examples codes on the main page. Any advise?
Thanks!

[alessandrofelder]

You can do this with the BrainGlobe Atlas API:

from brainglobe_atlasapi import BrainGlobeAtlas
atlas  = BrainGlobeAtlas("allen_mouse_100um")
print(atlas.structures_list)

What you are looking for is the "acronym" of each structure.
You can also do fancier things like querying for the children of a certain structure.

[Eddymorphling]

Thanks! @alessandrofelder Thats helpful.

Having issues with transparency for the brain regions/points and giving it a different color. Is this the right way to pass it?

# add the brain regions
region1 = scene.add_brain_region("CB", alpha=0.9, color="grey")
region2 = scene.add_brain_region("HY", alpha=0.9, color="blue")
region3 = scene.add_brain_region("TH", alpha=0.9, color="red" )

file_path ="/points/points.npy"
points = load_points_from_file(file_path)

filtered_points_region1 = filter_points_in_region(points, region1)
filtered_points_region2 = filter_points_in_region(points, region2)
filtered_points_region3 = filter_points_in_region(points, region3)

scene.add(Points(filtered_points_region1))
scene.add(Points(filtered_points_region2))
scene.add(Points(filtered_points_region3))

scene.content
scene.render(zoom=1)

This creates something like this where the added regions and points inside that region have the same color.

[adamltyson]

Are you wanting to change the properties of the points? If so that needs to be passed when you call Points, see this example:

brainrender/examples/brainmapper.py

Line 31 in e7d9be6

cells = Points(cells_path, radius=45, colors="palegoldenrod", alpha=0.8)

[adamltyson]

Also, @Eddymorphling if you have usage questions (rather than a bug report), would you mind asking your question over on the image.sc forum, tagging your question with brainglobe and the name of the tool you're using (e.g. brainrender). This makes it much easier for others to benefit from any advice. I'll close this issue, but feel free to ask as many questions as you like on the forum (ideally one post per topic). Thanks!

[Eddymorphling]

Are you wanting to change the properties of the points? If so that needs to be passed when you call Points, see this example:

brainrender/examples/brainmapper.py

Line 31 in e7d9be6

cells = Points(cells_path, radius=45, colors="palegoldenrod", alpha=0.8)

Thanks, @adamltyson. Actually, I would like to make the brain regions transparent. But that does not seem to work. I will start posting on the Fiji forum, sorry for the hassle.

[alessandrofelder]

FWIW @Eddymorphling there is a known issue with setting transparency #390 that seems to occur in some situations, but we haven't managed to reproduce fully.