I really like the MapMyCell tool! I would like to ensure I am correctly decoding the provided cell class and subclass abbreviations . There appears to be a table for this: Cell type references - brain-map.org. But the current link says: " * See what the abbreviations mean through this interactive table [FIX LINK]." And I cannot find what I am looking for. Any help would be much appreciated!
-Randall
Hi @reck999 ,
There is a separate page where we have enabled download of Excel spreadsheets decoding the acronyms used in our cell type taxonomies. Look for these buttons
on this page. They are in the “How to use ABC Atlas” section of the page.
Additionally (though I think this is not the answer to the question you are asking): the page pointed to by the “through this interactive table [FIX LINK]” in your post, namely
https://alleninstitute.github.io/abc_atlas_access/descriptions/WMB-taxonomy.html
is a Jupyter Book page documenting the official release of our Whole Mouse Brain taxonomy. If you click on the “annotation table” link in the second paragraph (see screenshot), you will download an Excel spreadsheet associating cell types, marker genes, and anatomical regions.
The link is not broken for me. If it is for you, please let us know, because that is a different concern.
Please reach out if anything is unclear.
Another of my colleagues has just updated the “…[FIX LINK]” link so that it also points to the spreadsheet decoding the cell type name acronyms. Hopefully this will avoid future confusion.
Thanks for calling this out.
Thank you!
Hi,
I have successfully run Mapmycells on my spatial MERFISH data. As an output, I now have information on class, subclass, cluster, and supertype for each cell. I would like to decode this information into different brain anatomical regions, such as the DG, MB, etc.
Could you please guide me on how I can obtain this information?
There is another thread about aligning MERFISH data to spatial locations here.
If you’d like to see where cell types are expressed in the brain in the mouse whole brain data hosted at Allen Brain Map, you could (1) visualize data on the ABC Atlas or (2) see top brain regions per cell type using Annotation Comparison Explorer in this configuration:
There currently is no direct way to align MapMyCells output (which is based on cell types) to specific anatomic structures.
Hi @jeremyinseattle,
Thank you for your response.
I believe I am in a similar situation to @reck999 (the original post created by him). I have identified the class, subclass, cluster, and supertype information from the Mapmycells output, and I would like to decode this information into anatomical brain regions.
For this, I am planning to use the file available at this link, which contains information on each class, cluster, and supertype, along with their corresponding anatomical brain regions.
Additionally, I believe the same file is used in the ACE Explorer.
Could you please confirm whether the procedure I am following is correct?
@danielsf Please provide your suggestions as well.
Thank you again for your help.
I misunderstood, I thought you wanted to know which cell types are in which brain region. If you just are looking for what the abbreviations for brain regions (and other components of the cell type names) mean, you can use this table.
