Indexing in the map my cells web tool

Technical
1

Hello,

I’d like to use the MapMyCells tool (Brain Knowledge Platform) in conjunction with spatial data. It is fairly straightforward to append the output of the MapMyCells tool to the anndata in Python. The question is - is the indexing of the cells kept the same after the map my cells process as it was in the anndata file? Or does anyone have an idea for how I could check? There are no other overlapping variables in the two data frames.

Thanks in advance! New to this and looking forward to learning.

2

The output of MapMyCells will include a column cell_id which is the index of the obs dataframe from the input h5ad file (so, whatever you get from my_anndata_obj.obs.index.values). This will allow you to join the mapping output with the original data (or, in your case, your spatial transcriptomics data).

If you want to see what else is included in the output you can see this page or this Jupyter notebook.

Let me know if anything is unclear.

3

Thank you so much for confirming the indexing stays consistent and for the additional resources! Very helpful.