Step 3: Automatic Segmentation
- Select the DAPI Individual Nuclei entry in the list and select the Segmentation Method for the class (Global Thresholding).
- The parameters for the class are displayed.
- In the Threshold section, set the Tolerance parameter to 1%.
- Click in the image on the blue-stained cell nuclei.
- The detected nuclei are overlaid in blue. The threshold values are displayed in the Threshold section in the Low/High input fields.
- Click on the areas of the blue cell nuclei that have not yet been detected until these have been completely overlaid.
- Set Fill Holes to On.
- This fills any holes in the detected cell nuclei.
- In the Separate section, select the Watersheds entry from the dropdown list and set the number to 3.
- Clear separation lines are now visible between the cell nuclei.
- Click Next.
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