Additional packages might be required. Therefore, conda environment files are provided, they can be installed using:
conda env create -f <environment-file.yml>
conda activate <your new env>
pip install git+https://github.com/royerlab/ultrack
The existing examples are:
- multi_color_ensemble: Multi-colored cytoplasm cell tracking using Cellpose and Watershed segmentation ensemble. Data provided by The Lammerding Lab .
- flow_field_3d: Tracking demo on a cartographic projection of Tribolium Castaneum embryo from the cell-tracking challenge, using a flow field estimation to assist tracking of motile cells.
- stardist_2d: Tracking demo on HeLa GPF nuclei from the cell-tracking challenge using Stardist 2D fluorescence images pre-trained model.
- zebrahub: Tracking demo on zebrafish tail data from the zebrahub acquired with DaXi using Ultrack's image processing helper functions.
- neuromast_plantseg: Tracking demo membrane-labeled zebrafish neuromast from Jacobo Group of CZ Biohub using PlantSeg's membrane detection model.
- micro_sam: Tracking demo with MicroSAM instance segmentation package.
To run all the examples and update the notebooks in headless mode, run:
bash refresh_examples.sh