Cell detection and measurements

Practice

3. QuPath cell detection

   1. Threshold-based cell detection

      1. Within the ROI created in 2, detect nuclei in the DAPI channel using QuPath’s built-in cell detection method

         • Use default parameters: how many nuclei are detected?

         • Change sigma used for the Gaussian method: how does the number of detected nuclei change?

         • Change the intensity threshold: how does the number of detected nuclei change?

         • Change the cell expansion (in microns): do you notice a difference in cell size?

      Tip 1: Re-running cell detection will overwrite existing detections.

      Tip 2: Start with default, make small changes then larger changes until obtaining a satisfying segmentation.

   2. Machine learning-based cell detection

      1. Within the ROI created in 2, detect nuclei in the DAPI channel using StarDist’s extension in QuPath

         • Use default parameters: how many nuclei are detected?

         • Change detection probability: how many nuclei are detected?

         • Compare segmentation results between threshold-based and ML-based cell detection (one way to do this is to run threshold-based nuclei detection in another ROI).