cell_detection script

[RVP20]

Hi there,
Thank you for Celloscope, I have been trying to run the method on a 10X Visium dataset on my MacOS 14.2.1. For this, first I have installed QuPath 0.5.1 and tried to run the script cell_detection.groovy to get an estimate of number of cells at each spot. I have added the path to my coordinates file and I have added a path to an output file. However, upon adding the image and then running the script, the output shows that 0 cells are detected at each spot. I am wondering if I am doing something incorrectly, since I have not used QuPath before. Will be grateful if someone can assist me with this.

Thanks!

[gerasa]

I used the procedure only for one data set so I do not have a vast experience, however, I can suggest trying different parameters here:

class WatershedCellDetectionConfig {
String detectionImageBrightfield = "Hematoxylin OD"
double backgroundRadius = 35.0
double medianRadius = 0.0
double sigma = 3.0
double minArea = 50.0
double maxArea = 1000.0
double threshold = 0.4
double maxBackground = 2.0
boolean watershedPostProcess = true
double cellExpansion = 5.0
boolean includeNuclei = true
boolean smoothBoundaries = true
boolean makeMeasurements = true
}

to adjust to your images.

Hints how to pick parameters can be found here:

Misc. QuPath tutorial 2 – IHC analysis. https://youtube.com/playlist?list=PL4ta8RxZklWk_O_Z7K0bZlhmHtaH73vlh.

Misc. QuPath tutorial: cell detection. qupath.readthedocs.io/en/stable/docs/tutorials/cell_detection.html.