Archive or Dearchive OME-Zarr¶

This task can be used to archive an OME-Zarr folder. All images contained in the folder will be first compressed to a higher compression level, the the full OME-Zarr will be archived to a unique TAR file for easier long-term archiving. The same task can also be used to later unarchive the OME-Zarr.

The task is not compatible with the Fractal server and can only be run locally.

Parameters¶

Below is a detailed explanation of important parameters.

Zarr URL¶

In the archiving mode (see the archive parameter), you need to provide the path to any image stored in the OME-Zarr folder you wish to archive. The full OME-Zarr folder containing the image will then be archived. Although counterintuitive, this is to ensure compatibility with the Fractal platform, which requires the path to an OME-Zarr image to be provided.

In the unarchiving mode (see the archive parameter), you need to provide the path to the TAR archive file containing the OME-Zarr folder you wish to unarchive. It will then be extracted the OME-Zarr in the same directory as the directory containing the TAR file.

Archive¶

This parameter can be used to run the task in archiving mode or in unarchiving mode:

    Archiving mode:  
        archive = True
    Unarchiving mode:  
        archive = False

Keep TAR Archive¶

In the dearchiving mode, you can choose to still keep the TAR archive file after unarchiving using this parameter. By default, the archive is kept after unarchiving.

Output Preview¶

By default, the task will create a downsampled version of the OME-Zarr folder called preview. This allows to still view the images contained in the OME-Zarr archive (which is unaccessible after archiving) at a much lower resolution than the original image, while drastically reducing the OME-Zarr folder size. With this parameter, you can choose to skip the creation of the preview.

Local Run Command¶

python run_archiving.py