OMERO download

Download images from OMERO server. Can download individual images (--images) or full dataset (--datasets) or project (--projects) folders.

Install

pip install git+https://github.com/cellgeni/omero-download.git

Usage

Basic use:

omero-download --images 123 456 789 --output_dir /path/to/download

If you don't want the Group-Project-Dataset structure to be created as folders you can use the --ignore_hierarchy flag to flatten all the paths.

Downloading dataset or project folders:

omero-download --projects 6969 --output_dir /path/to/download
omero-download --datasets 7337 8008 --output_dir /path/to/download

Sanger Farm Module

To simplify the complex dependency install that omero-py has, the tool is provided as a module so it can be use without installing anything.

$ module load cellgen/omero-download
** Using custom python for this environment
** See avaiable options using: omero-download -h

omero-download --images 123 456 789 --output_dir /path/to/download