Fractal task collection to run Segmentation Tasks
| Task | Description | Passing |
|---|---|---|
| Stardist Segmentation | Run Segmentation with pretrained/custom Stardist Model | ✓ |
| Seeded Watershed Segmentation | Performs segmentation (e.g., of cells) using a label image as seeds and an intensity image (e.g., membrane stain) for boundary detection. | ✓ |
To install this task package on a Fractal server, get the tar.gz release and install using Pixi.
To install this package locally:
git clone https://github.com/pelkmanslab/abbott-segmentation_tasks
cd abbott-segmentation_tasks
pip install -e .
For development:
git clone https://github.com/pelkmanslab/abbott-segmentation_tasks
cd abbott-segmentation_tasks
pip install -e ".[dev]"