mcd2zarr

Command line tool to convert MCD files to Zarr

Installation

Use the package manager pip to install mcd2zarr:

pip install mcd2zarr

Usage

Call mcd2zarr on the command line:

Usage: mcd2zarr [OPTIONS] MCD_FILE [ZARR_FILE]

  Convert MCD files to Zarr

Options:
  --zarr-version TEXT      Zarr version
  --ome-zarr-version TEXT  OME-Zarr version
  --version                Show the version and exit.
  --help                   Show this message and exit.

Zarr format

MCD file contents are extracted into the following Zarr structure:

myfile.zarr
├── .zattrs  (mcd_file, mcd_schema, slide_groups)
├── .zgroups
│
├── S01_SlideDescription
├── S02_SlideDescription
├── ...
└── Snn_SlideDescription
    ├── .zattrs  (slide_metadata, acquisition_groups, panorama_groups)
    ├── .zgroups
    │
    ├── A01_AcquisitionDescription
    ├── A02_AcquisitionDescription
    ├── ...
    ├── Ann_AcquisitionDescription  (in OME-Zarr format)
    │   ├── .zattrs  (acquisition_metadata, has_before_ablation_image, has_after_ablation_image)
    │   ├── .zgroups
    │   │
    │   ├── before_ablation_image  (optional, in OME-Zarr format)
    |   |   ├── .zattrs
    |   |   └── .zgroups
    │   │
    │   └── after_ablation_image (optional, in OME-Zarr format)
    |       ├── .zattrs
    |       └── .zgroups
    │
    ├── P01_PanoramaDescription
    ├── P02_PanoramaDescription
    ├── ...
    └── Pnn_PanoramaDescription  (in OME-Zarr format)
        ├── .zattrs  (panorama_metadata)
        └── .zgroups

Authors

Created and maintained by Jonas Windhager until February 2023.

Maintained by Milad Adibi from February 2023.

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

BodenmillerGroup/mcd2zarr