cellSAM Usage

Step-by-step Protocol for Using cellSAM

CellSAM Usage in Napari:

1. Load  image: 

• Go to File > Open File(s).

• Select your microscopy image (.tif, .png, etc).

2. Semi-Automatic Segmentation:

• Select the Bounding Boxes layer.

• Choose the Rectangle tool and select a region around the cell of interest.

• Click “Confirm Annot”. 

• The model will generate a segmentation mask.

• You can repeat this to segment multiple cells. 

• Click “Clear mask” to remove segmentations.

• Click “Reset” to restart completely.

3. Automatic segmentation: 

• Click “Segment All”.

• Wait for processing to complete.

• A new labels layer(Segmentation Overlay) will appear.

4. Save results:

• Select the segmentation labels layer. 

• Go to File > Save Selected Layer(s).