Cell detection problem

Hi all,

I’m a beginner user with QuPath, but since I started using the last version (0.2.0), I have been experiencing problems with the cell detection feature, I’m not sure of which kind. Here what I have been doing:

Using the brush tool, select the tumor areas and set the class as tumor.

Select an area with positive and negative cells > analyze > preprocessing > estimate stain vectors, not using the modal values > autodetect
Select the tumor annotation > Analyze > cell analysis > cell detection

I tried the cell detection both with the standard parameters and very permissive ones, without any luck.

Any ideas what I might do wrong or how I could solve this problem?
Alternatively, is there a way for me to import this project in the old version without losing all the annotations I did?

Many thanks in advance


You can’t really transfer projects between versions, but depending on your file type (some file types had a coordinate system change and this won’t work well), you could try to export and re-import just the annotations using a pair of scripts.

To determine the problems you are having with cell detection would require more information to troubleshoot. Some screenshots of what you are trying, what your Image metadata tab looks like, etc would be useful. Do you get a bar showing that the cell detection is being calculated? Could you have detection visibility turned off?

Hi, thank you very much for your answer. Here are two screens with the info you asked, and yes I get to see the progress bar once I hit run. I have also just managed to see very little detection points (in red in the second picture), which makes me think it is a problem of the parameters I input.

1 Like

Yep, the problem is with the Image metadata.
Normal pixels sizes for your image would be around 0.5 um or lower.

You can fix this in FIJI or potentially use the original image format (if there was an original image format). You will want to figure out what the actual pixel sizes should be first :slight_smile:

Thank you, that solved the problem. Unfortunately I still had to upload again the images in the QuPath project, and in doing so I lost all the annotations, but at least the cell detection now is working. Cheers!