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In each h5 file in the `patches` folder, there is a key called `coords` giving the coordinates of the **top-left** corner of the patch in the full resolution HE image.
In each h5ad file in the `st`…
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Hi,
The Xenium are imaging-based ST technology so that the Xenium dataset's spatial coordinates are not supposed to be grid.
Why does the TENX99 dataset have the grid coordinates.
I check the …
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Thanks a lot for such a great job, I would like to ask where is the training and testing code for the subsequent wsi classification
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Sorry for the late reply. Each fold is trained for a fixed number of epochs. There is no early stopping based on validation c-index (results wouldn't be fair).
_Originally posted by @…
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- Re-run code to see if its works with the provided datasets
- understand what it is trying to do
https://github.com/mahmoodlab/TOAD
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Hi all,
Thanks for providing this resource. Is there a way to match CellViT's cell type labels, obtained from the images, with the gene expression vectors in the AnnData object?
Merel
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From the meta data `hf://datasets/MahmoodLab/hest/HEST_v1_0_2.csv`, I can't find the [Xenium data](https://www.10xgenomics.com/datasets/xenium-ffpe-human-breast-with-custom-add-on-panel-1-standard) pu…
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Hi, based on the following lines, it seems gradient accumulation is not properly implemented:
https://github.com/mahmoodlab/HIPT/blob/a9b5bb8d159684fc4c2c497d68950ab915caeb7e/2-Weakly-Supervised-Su…
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I used something similar to [this](https://github.com/huggingface/pytorch-image-models/discussions/1232) to extract the attention scores for the penultimate layer, as explained in the caption for …
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Hi all, great work with this model. I would like to use it on some of our pancreatic images. Is there a Jupyter notebook or example page about how to structure the image directories to pass into CTran…