MicroSAM Usage

Step-by-step Protocol for Using MicroSAM

Micro-SAM Usage in Napari:

Once Micro-SAM is installed, follow these steps to segment your datasets:

1. Organize your data: 

• If you have multiple timepoints, these have to be processed separately. Organize your time-lapse datasets by grouping TIFF images by time points into separate folders. Each folder should contain all images for a single frame. 

2. Launch Micro-SAM from command line: 

• Open the command prompt and type the following commands to activate Micro-SAM: 

conda activate micro-sam

napari

3. Access the Micro-SAM Plugin in Napari: 

• Within Napari, navigate to: 

           Plugins > SegmentAnything for Microscopy > Annotator 3D

4. Open and Preprocess your stack: 

• Specify the model to use and select the directory where embeddings will be saved by clicking Select Directory.

5. Compute Embeddings: 

• Click on Compute Embeddings. 

• A new folder will be created for the output of each time frame.

6. Automatic Segmentation: 

• Click on the Automatic Segmentation button to generate the initial segmentations. 

• You can then adjust the parameters to optimize the segmentation results. 

7. Manual Segmentation Correction: 

• After automatic segmentation, you may need to manually correct errors. 

• To delete unwanted surfaces, use the syringe tool to click on the background and then select the surface to remove. 

• To create new cells, use prompts (e.g., rectangles or points), click on the cell of interest, and then apply changes across all Z slices by clicking Segment All Slices. 

8. Exporting Images: 

To export the image with labels in image format follow: 

• Select File > Save Selected Layers > Choose the following format “napari builtins labels (*.tif *.tiff *.bsdf. *im .*lsm .*npz .*pbm .*pcx .*pgm .*ppm .*stk)”. 

9. (Optionally) Combine Segmented Time Points: 

• After segmenting all frames, combine the segmented time points into a single folder. 

Import this folder into ImageJ to combine the time points into a single stack.