Trackastra Usage

Step-by-Step Protocol for Using Trackastra

Trackastra Usage in Napari: 

1. Launch Napari from command line: 

• Open the command prompt and type the following commands to activate Trackastra: 

conda activate trackastra

napari

2. Access the Trackastra plugin in Napari: 

• Within Napari, go to: 

• Plugins > Trackastra tracking (trackastra)

3. Import your data:

• Load your files: 

• File > Open File(s)

• You must provide: 

• A timelapse image

• Corresponding masks

4. Select model and linking mode:

• You can use pretrained models or your own trained model.

• Choose a pretrained model:

• ctc

• general_2d

• general_2d_w_SAM2_features

• Choose a linking model: 

• greedy_nodiv(greedy linking with no division)

• greedy(greedy linking with division)

• ilp(ILP based linking): slower but more accurate.

3. Run tracking: 

• Run the tracking process from the plugin interface. 

4. Export results:

• The plugin generates:

• Relabeled masks

• Cell tracks

• You can export results in formats such as:

• CTC

• GEFF