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Virtual Analysis Environment

The IDR Virtual Analysis Environment (VAE) supports the open and reproducible analysis of data in the IDR. It is built on JupyterHub and is available to anyone interested in exploring and mining the diverse and vast range of image data and metadata in the IDR.


All notebook sessions are subject to available resources, are limited in the network resources they can access, and will automatically terminate after a period of inactivity. Do not store anything you wish to keep.

If you have any queries about the VAE, including questions about usage, API access and available data, please open an issue on the idr-contrib/community GitHub repository.


Public access

We have a set of Jupyter Notebooks that can be run by anyone without a login.


GitHub login

If you are interested in developing your own data analysis notebooks on our analysis platform please contact us with your GitHub username. This will give you more computational resources including scratch storage space than is available through the public access.

We will do our best to maintain this scratch space across upgrades of the VAE, though in the event of unforeseen issues we may need to delete all scratch space, and you should consider it as suitable for temporary storage only. Your scratch space may be deleted without warning if you have not logged in for over a month.

If as part of a planned update we need to delete our existing storage we will give at least one week's notice on idr-contrib/community and the @IDRstatus Twitter feed.


Elixir AAI login

If you have an Elixir AAI account you can use it to access the analysis platform. This is currently a demonstrator, and is identical to the public access. Please note that we are unable to investigate authentication errors between your chosen identity provider and Elixir AAI.


More information

For more information about the IDR please see the IDR home page.

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OMERO is distributed under the terms of the GNU GPL. For more information, visit openmicroscopy.org