Counting cells in a stack

Hi, I have a .lif file and was wondering what the best way to count the cells in this case would be. Qupath imports the image as a stack but it makes no sense to count cells in each z plane. Is there a way to display a maximum projection so I can just count the cells in a 2D image?

I believe you would want to generate the MIP prior to importing it into QuPath if that is what you want to analyze. While QuPath is now capable of generating whole slide images and has always done some exporting, it isn’t really image manipulation software. You are probably best off adjusting any images (splitting, cropping, stitching, MIP) in the original software prior to analysis.

In theory it should be possible to generate at least a downsampled floatprocessor, I guess, but that would take a lot of scripting for something that it likely more easily (and accurately) done elsewhere. As ever, with scripting, many things are possible if you take enough time :slight_smile:

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Thanks for the reply! Will look for another software to generate the MIP then.

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