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BlueBrain / atlas-densities

Tools to compute densities in the context of brain atlases.
Apache License 2.0
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Missing data for some brain regions in visual area #83

Open gaole2019 opened 1 month ago

gaole2019 commented 1 month ago

Hi, I want to know the estimated count and density of cell types in mouse visual area. But, I checked the website (https://bbp.epfl.ch/nexus/cell-atlas/) and found that the data for VISli (Laterointermediate area), VISpor (Postrhinal area), VISa (Anterior area), and VISrl (Rostrolateral visual area) is not available. So, how can I get these missing data? Thanks. image

mgeplf commented 1 month ago

I think @drodarie will have to comment, as I am not knowledgeable about this.

drodarie commented 1 month ago

Hi @gaole2019, The cell atlas version on the bbp website leverages a version of the annotation atlas that is closed to the Allen CCFv2 (2011). The brain regions you are referring to have been introduced (annotated) in the Allen annotation atlas with the CCFv3 version (2015-2017-2022). If you want to obtain the estimates for these brain regions from the BBP Cell atlas, you would have to run the pipeline again with the CCFv3 annotation volume. Find more information on this matter, in this paper

gaole2019 commented 4 weeks ago

@drodarie Ok, I got it. I will try to run the pipeline with the Allen CCFv3 annotation volume. Thank you very much!