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mahmoodlab / HEST

HEST: Bringing Spatial Transcriptomics and Histopathology together - NeurIPS 2024
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About cell type information #35

Closed nkuweili closed 3 months ago

nkuweili commented 3 months ago

Hi authors!

Thanks for your brilliant work! I also want to know where we can find the meta data of cells like cell type in HEST? Thanks! I am looking forward to your reply.

Best, Wei

guillaumejaume commented 3 months ago

Hi, the CellViT output is in https://huggingface.co/datasets/MahmoodLab/hest/tree/main/cellvit_seg. You can directly use the GEOJSON to viz the segmentation/classification with QuPath. Please note that CellViT output is not ground truth. Let me know if you have additional questions.

nkuweili commented 3 months ago

Thanks Guillaume,

Great. I fully agree with you that CellViT enables joint instance segmentation and classifcation of each nucleus into fve classes. While for those datasets which were provided with like "ground-truth" labels labeled by their pathologist, did HEST include these information? (I do agree that this type of information may not be easily accessible to collect.) Thanks for your time:)

guillaumejaume commented 3 months ago

There is no "true ground truth" shared as part of HEST at the moment. Cell phenotyping using the ST profile is doable. We will make a release with those in the next couple of weeks.

nkuweili commented 3 months ago

Great and thanks for detailed reply!