'Sample Id' of selected cells in MERFISH datasets in the online viewer don't match cell labels in h5ad data

How To Allen Brain Cell (ABC) Atlas
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Hi! I’ve been using the Brain Knowledge Platform to play with the MERFISH whole mouse brain data, and I have a question about the Sample Id annotation when using the Cell Selection tool. When selecting a few cells, it opens a panel on the right side of the screen with information on the selected cells, where we can see a Sample ID that looks like this: ‘18fa5e5b-e460-4c30-8f95-2ea4e8390e1b’ . I want to check the entire data for this cell from this experiment, but in the h5ad file I accessed in the AWB bucket, the cell_label information does not match the Sample Id at all. Could you please provide more information on how I can find the full transcriptomic data for the cells I selected in the MERFISH viewer?

Thank you!

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I would also be interested in an answer to this question.

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Hi @paulacauhy,

Thank you for your interest in ABC Atlas and thank you for your patience with this delayed response. The inconsistency in labeling between the downloadable data and that available in the ABC Atlas cell selection view is a known limitation. To help bridge this gap we have just published linking tables and an associated notebook to guide you in using them. Please find it here: Using cells selected in the ABC Atlas with Gene Expression data. — Allen Brain Cell Atlas - Data Access

Please let me know if there’s anything else we can do to make your experience better.

Best,
Elysha Fiabane
Product Manager, Allen Institute for Brain Science