QuPath: Cell Detection

[@ppcyj]

Thank you so much! I am struggling with qupath for IF image analysis. During cell detection some clutered cells are detected as one cells, and sometimes a large cell is segmented into multiple cells, could you let me know how can I adjust this?

[@johanna.m.dela-cruz]

Hi @ppcyj. You might have to adjust sigma. Try different values to see which one would give you best detection.

[@sanyamjain4210]

Thank you for the video! My pixel width/height doesn't fall in the given range. It is way out 352 um :" what should I do for counting then?>

[@johanna.m.dela-cruz]

Hi @sanyamjain4210. Are your files large? If they are not really whole slide images, perhaps you can open your files in Fiji and use StarDist to segment the cells. Also, is the pixel size really that large? Perhaps there might be something wrong with the spatial calibration in your image.

[@michaels.nelson8237]

I would recommend correcting the pixel height and width in the Image tab to whatever settings are correct from the microscope. Most microscope formats will include this information, but manipulating the image through other software or export to other formats can lose the original information. Posting to the image sc forum is also a great option for quick responses!

[@KathleenMoore-w6q]

Dalton Ridge