Step-by-Step Protocol for Using Trackastra
Trackastra Usage in Napari:
Launch Napari from command line:
Open the command prompt and type the following commands to activate Trackastra:
conda activate trackastra
napari
Access the Trackastra plugin in Napari:
Within Napari, go to:
Plugins > Trackastra tracking (trackastra)
Import your data:
Load your files:
File > Open File(s)
You must provide:
A timelapse image
Corresponding masks
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.
Run tracking:
Run the tracking process from the plugin interface.
Export results:
The plugin generates:
Relabeled masks
Cell tracks
You can export results in formats such as:
CTC
GEFF