Pipeline to track movies from Thunder with Ultrack. Prepares for using Track Gardener.
00_lif_to_zarr.ipynb
input:
- lif file containing a movie to be tracked
output:
- channels of the movie saved as separate zarr files
01_segment_test_and_view.ipynb
- this is an optional step to easily check different segmentation approaches
- by choosing start and stop accross dimensions select a small subset for tests
input:
- channel to be tracked (zarr)
output:
- None
02_segment.ipynb
input:
- channel to be tracked (zarr)
output:
- segmented masks (zarr)
- dir with png masks (can be deleted)
03_run_ultrack.ipynb
- run in the environment dedicated to ultrack
- use gurobi optimizer if possible
input:
- masks (zarr)
ouput:
- database with the tracking solution (Ultrack format)
- optional: masks labeled by tracks (zarr)
04_view_tracking.ipnb
- a short script to visualize tracked labels in napari