3D Multiplexed Image Analysis Task Collection
| Task | Description | Passing |
|---|---|---|
| Convert Cellvoyager Multiplexing to existing OME-Zarr | Converts CV7000/CV8000 images and extends to existing OME-Zarr file. | ✓ |
| Convert Abbott-legacy H5 to OME-Zarr | Converts H5 files in abbott-legacy format to OME-Zarr files | ✓ |
| Compute Registration (elastix) | Compute rigid/affine/b-spline registration for aligning multiplexed 3D images across cycles. | ✓ |
| Apply Registration (elastix) | Apply rigid/affine/b-spline registration to images. | ✓ |
| Compute Registration (warpfield) | Compute warpfield registration (see https://github.com/danionella/warpfield) for aligning multiplexed 3D images across cycles. | ✓ |
| Apply Registration (warpfield) | Apply warpfield registration. | ✓ |
| Compute Channel Registration (elastix) | Compute similarity registration of all channels in an acquisition to a reference channel. | ✓ |
| Apply Channel Registration (elastix) | Apply similarity registration to multi-channel acquisition. | ✓ |
| Stardist Segmentation | Moved to abbott-segmentation-tasks | ✓ |
| Seeded Watershed Segmentation | Moved to abbott-segmentation-tasks | ✓ |
| Upsample Label Image | Upsamples label images to the highest image resolution. Useful if segmentation was peformed on e.g. level 1 to avoid resolution mismatch in downstream tasks. | ✓ |
For Feature Extraction, see abbott-features
Important
Warpfield Registration Tasks currently only run with CUDA > 11.x.
To install this task package on a Fractal server, get the whl from the Github release and use the local task collection.
To install this package locally:
git clone https://github.com/pelkmanslab/abbott
cd abbott
pip install -e .
For development:
git clone https://github.com/pelkmanslab/abbott
cd abbott
pip install -e ".[dev]"