Fetch scripts for retrieving screen data from the OMERO IDR project - http://idr-demo.openmicroscopy.org.
fetch_omero_data is used to download all metadata for a screen. The output is a tab delimited flat file of all metadata fields (including annotations) and each associated well image.
Annotations are retrieved from the OMERO API as key-value pairs and transformed into columns in the resulting data set.
This simple structure allows the data to be used with other applications.
fetch_omero_images is then used to retrieve all images using the OMERO id.
Currently based on the public endpoints at http://idr-demo.openmicroscopy.org and so does not yet include functionality to authenticate against a secure server.
Use pip to install requirements:
$ pip install -r requirements.txt
Fetches metadata for a screen and saves it as a tab separated file
$ python3 fetch_omero_data.py --id 102
Parameters:
id [required]: the unique identifier of the screen
output: File name of the tab delimited flat file (default idr.tab)
url: URL of the OMERO server (default http://idr-demo.openmicroscopy.org)
Fetches images for a screen
$ python3 fetch_omero_images.py --output images
Parameters:
output [required]: Path to the directory where the images will be saved
data: Path to the tab delimited flat file generated by fetch_omero_data.py (default idr.tab)
url: URL of the OMERO server (default http://idr-demo.openmicroscopy.org)