# mcd2zarr
Command line tool to convert MCD files to Zarr
## Installation
Use the package manager [pip](https://pip.pypa.io/en/stable/) to install mcd2zarr:
```
pip install mcd2zarr
```
## Usage
Call `mcd2zarr` on the command line:
```
> mcd2zarr --help
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_SlideDescription01
├── S02_SlideDescription02
├── ...
└── Snn_SlideDescriptionNN
├── .zattrs (slide_metadata, acquisition_groups, panorama_groups)
├── .zgroups
│
├── Ann_AcquisitionDescriptionNN
├── A02_AcquisitionDescription02
├── ...
├── Ann_AcquisitionDescriptionNN (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_PanoramaDescription01
├── P02_PanoramaDescription02
├── ...
└── Pnn_PanoramaDescriptionNN (in OME-Zarr format)
├── .zattrs (panorama_metadata)
└── .zgroups
```
## Contributing
Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.
## License
[MIT](https://github.com/BodenmillerGroup/mcd2zarr/blob/main/LICENSE)
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