Can Cellpose be used to segment cell in the HE-stained images ?

[februaryfang]

Hi Cellpose Team,

I have a question regarding the use of Cellpose3 for a specific application. Recently, single-cell spatial transcriptomics and single-cell spatial HD technologies (e.g., 10x Genomics Visium) have become very popular. These technologies typically report data in units of spots or bins, which represent the average gene expression of all cells within a specific region.However, I have a requirement to identify individual cells from the corresponding HE-stained tissue images and obtain cell-level results. Specifically, I need to segment and identify each cell in the HE-stained images.Can Cellpose be used to achieve this? If so, are there any specific considerations or best practices for using Cellpose with HE-stained images?
Thank you for your help!

Best regards, februaryfang

[carsen-stringer]

I have not seen the visium data myself, but the merscope data works with cellpose, they have it integrated in their post-processing pipeline, which is open-source: https://github.com/Vizgen/vizgen-postprocessing

I would recommend retraining a model if it looks like cellpose isn't working well out of the box on your data. if you want to provide images + segmentations we can provide advice