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

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

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

Export OMERO ROIs and their polygon, polyline, rectangle, ellipse, line, point and text shapes to one JSON file per image without downloading the images:

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

To download the original images and export their annotations in the same run:

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

Each JSON file contains image metadata (OMERO ID, name, description, dimensions, physical pixel sizes and Group/Project/Dataset hierarchy), ROI metadata, and all shapes belonging to each ROI. Shape plane, styling and affine transform properties are included when available. Polygon and polyline points are stored both as parsed [x, y] arrays and as the original OMERO points string.

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