https://github.com/cellgeni/omero-download
Download images from OMERO server
https://github.com/cellgeni/omero-download
Last synced: 5 months ago
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Download images from OMERO server
- Host: GitHub
- URL: https://github.com/cellgeni/omero-download
- Owner: cellgeni
- License: agpl-3.0
- Created: 2025-03-03T23:53:04.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-03-05T13:45:18.000Z (over 1 year ago)
- Last Synced: 2025-09-09T23:51:32.168Z (9 months ago)
- Language: Python
- Size: 17.6 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# OMERO download
Download images from OMERO server. Can download individual images (`--images`) or full dataset (`--datasets`) or project (`--projects`) folders.
# Install
```shell
pip install git+https://github.com/cellgeni/omero-download.git
```
# Usage
Basic use:
```shell
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:
```shell
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.
```shell
$ 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
```