Upload images in OMERO¶
OMERO.insight¶
A comprehensive overview on the upload procedure using OMERO.insight can ve found in the following material:
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
Python and Jupyter Notebooks¶
It is possible also to upload your data using the Python API. We highly suggest to use the package ezomero. Documentation for this package can be found here. Furthermore, the RDM opened a GitLab repository containing all the different informations plus step-by-step Jupyter Notebooks to upload your data.
NOTICE: The Jupyter Notebooks (JN) can be run on your local machine, or remotely on Helmholtz Jupyter Lab or Galaxy. Please, contact Riccardo Massei for further info on how to run your JN remotely.
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!
Other Strategies - FiJi, Napari CellProfiler¶
In case you are using FiJi, Napari CellProfiler for your data analysis, it is possible also to directly upload your data into OMERO using a special plugins.
For other inputs, please contact the RDM team.