Calibration, deskewing, deconvolution, registration, and fusion for qi2lab opm-v2 OME-Zarr acquisitions.
Read the documentation, starting with installation and the first workflow.
Requires Python 3.12 and uv. Windows and Linux installations include CUDA dependencies by default; Windows also requires the cuCIM setup.
uv sync
uv run process "/path/to/acquisition" --deconvolve
uv run fuse "/path/to/acquisition"
uv run export-ome-tiff "/path/to/acquisition"Each command's reference describes its arguments, options, and an example.
Append --help to any command for its installed options and defaults.
| Command | Purpose |
|---|---|
| inspect-opm | Inspect acquisition metadata. |
| process | Calibrate, deconvolve, and deskew. |
| fuse | Register and blend processed tiles. |
| display | View outputs and select an ROI. |
| process-ROI | Process and fuse selected raw regions. |
| export-ome-tiff | Export fused images as compressed OME-BigTIFF. |
| export-projections | Export annotated projections and movies. |
| encode-projections | Encode existing projection TIFFs as movies. |
| convert-timelapse | Export raw scan-plane timelapses. |
See contributing, running tests, and simulation examples.
Preview the documentation in a separate environment:
uv venv .venv-docs --python 3.12
uv --no-config pip install --python .venv-docs --group docs
uv run --python .venv-docs --no-project mkdocs serveBSD-3-Clause licensed; see LICENSE.