StarDist Usage

Step-by-step Protocol for Using StarDist

StarDist Usage in Napari: 

Once StarDist is installed, follow these steps to segment your datasets: 

1. Launch StarDist from command line: 

• Open the command prompt and type the following command to activate StarDist: 

napari

2. Access the StarDist Plugin in Napari: 

• Within Napari, navigate to: 

▪ Plugins > Stardist-napari

3. Open an Preprocess your stack:

• Specify the model to us: 2D or 3D or custom (select the directory where it was saved the pretrained model)

4. Automatic Segmentation: 

• Click Normalize Image

• Click Shown CNN Output

• Click Run

5. Viewing Single Segmented Cells: 

• After the segmentation, select the cells or regions of interest from your image or the segmentation results. 

6. Save the segmentations: 

• Choose a location on your computer to save the exported file. 

• Name the file and ensure it has the correct extension.

Click Save to export the statistics.