Updated 12/07/21: This repository is the current code base for the following projects, which have been merged into this project:
These repositories have been superseded by this one and are no longer updated
This toolkit includes Docker files and software utilities designed to assist researchers to deposit their microscopy data into an OMERO server.
The Docker files in the toolkit provide support for uploading to and querying OMERO servers, the Open Microscopy Environment image data repository platform. The Docker files are duplicated from the original OMEROConnect repository.
A project providing Python code for uploading data and metadata from a local file structure into an OMERO server instance.
Included with the toolkit are two main utilities for supporting (meta)data deposition and curation activities: the 'tag manager' and the 'batch upload' scripts.
The toolkit is intended to be deployed as Docker containers. There are three container images: omero_base, omero_uploader and omero_jupyter. The Jupyter Docker container image inherits from the uploader image which in turn inherits from the base image.
The easiest way to use the toolkit is simply to pull and run the pre-built Docker images that are provided by the OMEROConnect project. Pull the latest images with the following command:
docker pull biordm/omero-connect:omero_uploader
docker pull biordm/omero-connect:omero_jupyter
Once the OMEROConnect images are downloaded to the local Docker image repository, they can be run with slight modifications to the commands given previously, for instance:
docker run -t -d --name omero-uploader -v /C/projects/Omero_data:/var/data/omero_data -v /<path>/<to>/<omero-toolkit>:/home/jovyan/omero-toolkit --entrypoint /bin/bash biordm/omero-connect:omero_uploader
docker run --name omero-jupyter -p 8888:8888 -v 'D:\projects\omero_connect_demo\notebooks:/home/jovyan/work/query_notebooks:rw' -v /<path>/<to>/<omero-toolkit>:/home/jovyan/omero-toolkit omero_jupyter
To access a bash terminal in the resulting Docker containers, run commands such as:
docker exec -it omero-uploader /bin/bash
Please see the README.md in the docker directory for instructions on building
the Docker images yourself.