ABC Atlas Spatial Transcriptomics Beta - class names

Hi there,

I was using the ABC beta today (spatial transcriptomics cellular atlas) I can’t seem to find descriptions or elaborations on the names of the individual classes - more specifically, what these names mean/represent. Is this somewhere in the database’s documentation or is it in your preprint? Please let me know.

Also, it would be nice to make the UMAP in the 10xgenomic data interactive (i.e., hovering over the specific region when colourised a specific way will tell you what the colour represents and what you’re looking at). One feature I would really like to see, in addition to UMAP interactivity, is the ability to visualise results for multiple genes.

Happy to provide more information about my experience with the ABC beta if you’d like!

Hi @MPanday,

Thank you so much for your interest in the ABC Atlas and for your feature suggestions! A detailed discussion of the cell classification system is indeed available in the preprint. We also have resources available on GitHub which offer an opportunity to learn about the whole-mouse-brain taxonomy through interactive tutorials.

Product Manager, ABC Atlas

1 Like

Thank you very much, @Elysha-AIBS ! I appreciate the information. Though in a future build, another feature that might be helpful is a page with the names of the classes and what they mean/represent. For example :

oligo = oligodendrocyte,
but then further delineation of

  • oligo NN and the nested classes within
  • oligo OPC and the nested classes within

Just a page to name the classes fully so a user would know what they are selecting when filtering by class. Would it be possible to provide such a list to this forum now, or in the immediate short term?

1 Like