Ultrack Usage

Step-by-step Protocol for Using Ultrack

Ultrack Usage in Napari

1. Launch Ultrack from the command line: 

• Open the command prompt and run the following commands to start Napari with Ultrack: 

conda activate ultrack 

napari

2. Open your datasets:

• Go to File > Open File(s) to open individual files. 

• Use File > Open Files as Stack to open multiple images as a stack. 

• If possible, use segmented datasets for improved tracking results. 

3. Select the desired Ultrack workflow: 

• Automatic tracking from image: track cells directly from a sequence of images. 

• Automatic tracking from segmentation labels: track cells using pre-existing segmentation labels.

• Manual selection of inputs: use precomputed cell detections and contour detections.

4. Show advanced settings: 

• Pre-processing: prepare images before segmentation.

• Segmentation: detect objects in each frame.

• Linking: connect objects between consecutive frames. 

• Tracking: build trajectories for objects across all frames.

Adjust the parameters as needed to optimize the results, then click Run.

5. Export results: 

• Once the process is complete, Ultrack generates the following outputs:

• Foreground

• Contours

• Segments

• Tracks

• Tracks can be exported in several formats, including: 

• .csv

• .xml

• .zarr

• .dot

• .json