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TIO-IKIM / CellViT

CellViT: Vision Transformers for Precise Cell Segmentation and Classification
https://doi.org/10.1016/j.media.2024.103143
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Application to non-contiguous patches #39

Closed florianbuettner closed 4 months ago

florianbuettner commented 4 months ago

Hi, very interesting work and thanks for sharing the code! I would like to test CellVit on a set of non-contiguous patches (1024x1024, 0.25 Micrometer) from different WSI. Should I start with cell_segmentation/inference/inference_cellvit_experiment_pannuke.py and adapt it if necessary? Is it advisable to perform a stain normalization beforehand? Thanks!

FabianHoerst commented 4 months ago

Hello,

exactly, you could use this or the MoNuSeg Inference Code. I have not compared the performance with and without stain normalization, but from Intuition, I would use it.