Hello
Regarding your statement: “While in the Cell Selection view, details of the selected cells can be downloaded as a csv file. Please note, only the first 100 cells will be included in the download. Full dataset download is available via GitHub.” . I couldn’t find the CSV file containing Anatomical Structure information for all cells on GitHub. Could you please provide the detailed path?
Rsbdz
What dataset(s) in particular are you exploring*? This will help us give you the right example piece of code to get you unstuck.
*examples of datasets:
Yao et al. whole mouse brain 10x RNAseq data
Yao et al. whole mouse brain spatial transcriptomics (MERSCOPE) data
Zhuang et al. whole mouse brain spatial transcriptomics data
Siletti et al. whole human brain 10x RNAseq data
etc.
Yao et al. whole mouse brain spatial transcriptomics (MERSCOPE) data.
The MERSCOPE data was registered to the Allen CCF (Common Coordinate Framework), meaning each cell as 3 dimensional coordinates associated with it and those three dimensional coordinates have anatomical annotations associated with them. Those coordinates and annotations exist in separate tables.
This Jupyter notebook shows how to join the two tables and associate cells with anatomical annotations.
Does that help?
I’m grateful for your guidance.