Have region name in surface layer metadata

[alessandrofelder]

Naming convention for region meshes is and ending in abbreviation, e.g....CB_mesh. Maybe region name should be in metadata so it displays in the tooltip?

[kiratoyoshihara]

@alessandrofelder

I don't know if I can, but can I work on this problem?

[kiratoyoshihara]

Hi @alessandrofelder

I have a rough idea of taking the name attribute from the following structure and adding it to the surface layer.

STRUCTURE_TEMPLATE = {
"acronym": "VIS", # shortened name of the region
"id": 3, # region id
"name": "visual cortex", # full region name
"structure_id_path": [1, 2, 3], # path to the structure in the structures hierarchy, up to current id
"rgb_triplet": [255, 255, 255], # default color for visualizing the region, feel free to leave white or randomize it
}

Do you think this is going to work out? 🤔

[alessandrofelder]

Yes, you are welcome to tackle this, but I am not sure this issue is even possible 😢 so tackle this at your own risk ⚠ it may require major surgery to the code!

Let me clarify (and modify) the issue a bit:

This is the current situation:

You can see in the layer list on the lower left, that the layer name and the tooltip of the layer are the same. I don't think it is possible to change this. Maybe you can find out?

Alternatively, we might be able to change the tooltip when we hover over a surface layer in the 3D view, similarly to what we do for 2D view currently. Then we could incorporate some custom tooltip text in the layer metadata, and display it in the 3D view. This might work, but the only way to know for sure is to try :)

[alessandrofelder]

In terms of what the tooltip text should be, we suggest (for now):

• change the Surface layer name to be the name of the region
• make the tooltip text a formatted string like f"{name} ({acronym}) ({atlas_name})" so for example "Diencephalon (Di) (Eurasian Blackcap)" in the screenshot above

[kiratoyoshihara]

I was thinking almost the same thing!
I'll see if I can do it as I have an idea of how to implement it. Thanks for the advice!

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/brainmapper-show-brain-regions-on-napari/110715/10