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mahmoodlab / HEST

HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024
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Regarding the Number of Patches and Spots in Xenium Dataset #60

Closed Yoyiming closed 4 weeks ago

Yoyiming commented 1 month ago

Hi, I noticed that in the Xenium dataset, the number of patches in the patches file is less than the number of spots in the st file. For example, in the TENX133 dataset, there are 3,811 spots, but only 1,377 patches in the TENX133.h5 file. Could you help explain the reason for this difference? Maybe I missed something important.

Thanks in advance!

guillaumejaume commented 1 month ago

Hi,

This is the spatial plot for TENX133: https://huggingface.co/datasets/MahmoodLab/hest/blob/main/spatial_plots/TENX133_spatial_plots.png, And this is the patching: https://huggingface.co/datasets/MahmoodLab/hest/blob/main/patches_vis/TENX133_patch_vis.jpg

As you can see, the tissue is not covering 100% of the image, hence the difference. Let me know if unclear.

Yoyiming commented 4 weeks ago

I understand your point now. Thanks again!