Step 3: Automatic Segmentation
- Click on the Individual Nucleus entry in the list and select the Segmentation Method for the class (Global Thresholding).
- The segmentation parameters (Smoothing, Sharpen, etc.) are displayed below the list.
- In the Smoothing section, select Gauss from the dropdown list and set the parameter Sigma to 1.5.
- Click on the blue-stained cell nuclei in the image.
- 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.
- In the Separate section, select the Watersheds entry from the dropdown list and set the number to 17.
- Clear separation lines are now visible between the cell nuclei.
- Click on the Individual Signal entry in the list.
- The segmentation parameters are displayed below the list.
- In the Smoothing section select Gauss from the dropdown list and set the parameter Sigma to 1.5.
- Click in the image on the green-stained signals.
- The detected signals are overlaid in green. The threshold values are displayed in the Threshold section in the Low/High input fields.
- Click on the areas of the green signals that have not yet been detected until these have been completely overlaid.
- Set Fill Holes to On.
- This fills any holes in the detected signals.
- In the Separate section, select the Watersheds entry from the dropdown list and set the number to 17.
- Clear separation lines are now visible between the signals.
- Click Next.
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