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mahmoodlab / HEST

HEST: Bringing Spatial Transcriptomics and Histopathology together
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TENX98 and TENX97 don't have pixel/array coordinates #28

Closed KalinNonchev closed 1 month ago

KalinNonchev commented 1 month ago

Hi, thank you for providing these valuable datasets. I have been exploring the breast cancer IDC dataset and noticed that samples TENX98 and TENX97 do not have pixel and array coordinates in their obs metadata. Could you clarify whether these coordinates are missing, or if this might be due to a preprocessing error? Thank you in advance! Best,

pauldoucet commented 1 month ago

Hello Kalin, For now we store the spot coordinates in the obsm['spatial'] for compatibility with some core scanpy methods such as sc.pl.spatial. First column and second column in obsm['spatial'] are x and y pixel coordinate in the full resolution H&E respectively.

KalinNonchev commented 1 month ago

Ok, I wrongly assumed that I would be able to find this also in the obs for all samples (named as array_row; array_col, pxl_row_in_fullres, pxl_col_in_fullres). Thanks