QuPath cell detection

I am having some issues with QuPath and cell detection. Here is a sample image.

test3.ome.tif (4.7 MB)

If I perform a simple / default cell detection it completely misses the cells and instead detects the background for some reason. How do I correct this?


I suspect the image type has been set to fluorescence… perhaps automatically because the image is rather dark. You can set it to brightfield under the ‘Image’ tab by double-clicking on the image type entry.

There is some more info at https://github.com/qupath/qupath/wiki/First-steps#seeing-the-image-properties or in the video tutorials.