Add metadata in OMERO - Tags and K/V Pairs¶
OMERO.insight¶
OMERO.web¶
You can easily upload K/V Pairs and Tables using OMERO.web scripts. These can be run in the top right menu in OMERO.web clicking on the grinding symbol.
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omero.web script for K/V pairs: “UFZ / Import from CSV” (Walktrough)
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omero.web script for Importing tables: “omero / import script” (Walktrough)
Command Line Interface (CLI)¶
A conda environment with omero-py need to be installed locally to use the CLI. Further explanation on how use the CLI are give on the OMERO documentation:
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Information on how to install miniconda are given here
- Information on how to install omero-py are given here
Jupyter Notebooks¶
It is possible also to attach metadata using the Python APi. We highly suggest to use the package ezomero. Documentation for this package can be found here. Furthermore, we open a GitLab repository containing all the different informations plus step-by-step Jupyter Notebooks (JN) to upload your data. NOTICE: The Jupyter Notebooks can be run on your local machine OR remotely at the Desy Jupyter Lab. Please, contact Riccardo Massei for further info on how to run your JN not locally.
Galaxy Project¶
Recently we developed a set of Galaxy Tools to upload images and metadata into a target OMERO instance. Please consult this training material to get more insight on how transfer data into OMERO using Galaxy!
Check out the Galaxy UFZ instance to run these OMERO tools!