I have fluorescence images for spheroids structures and I am interested in measuring the lumen area and the whole spheroid area. I tried to do so using image J but wasn’t able to get the right thresholding to detect lumens. Now, I moved to use the positive cell detection tool in qupath which looked a bit promising in terms of lumen detection, but now I am facing 2 problems:
1 - Lumen and spheroid detection wan’t accurate, I tried to change the parameters but didn’t have much effect (image attached).
fluorescence image.tif (333.4 KB)
spheroid-gp135-dapi_z12c3 4.tif (6.0 MB)
2- Each image has different analysis parameter and having hundreds of images makes the analysis more complicated time consuming
Since I am pretty new to qupath is there a better tool in qupath that I can use for lumen detection?
Thank you for your help!