Open Microscopy Environment

Hello,

While using OMERO in our server, we reached a novice question; why on earth do we need OMERO.insight (standalone application) to upload images?

For uploading, authentication is required. The implementation of this would make the workflow a lot simpler.

Best,
Kouichi

Dear Kouichi,

Especially since OMERO 5.3.0 in which OMERO.cli stopped being supported for Windows users and OMERO.insight shifted to maintenance mode, a web-based importer is definitely something that we would truly love to provide and we have done a little investigatory groundwork. However, at least without community contributions, I am afraid that it won't be coming soon: it's technically challenging. OMERO.insight has the advantage of being able to use Bio-Formats' "used files" to understand how to tie files together into images when there are many images and files locally to upload. OMERO.server's import process currently expects the client to group sets of files into filesets* so that they are stored and read together as necessitated by the image format. As Bio-Formats' readers are implemented in Java it is not easy for OMERO.web to query it in a similar manner.

* https://docs.openmicroscopy.org/latest/ ... l#filesets

Cheers,
Mark

Thank you for the prompt reply. And I'm glad to hear that the work is already in progress.

I wish I could help you there, but the matters appear beyond my expertise. I'll keep an eye on the progress. Do you have a Trello card for this?

Hi again, Kouichi,

at the moment there's no single card or board for "web import" since it will be quite a process, though one can definitely find a number of high-level requests like the one from last year's users' meeting or a sysadmin questionnaire.

The first step on the path to getting a web-based import, though, is the Python library for importing. There is a card for that, and Will has been collecting his various suggestions from the forums under https://gitlab.com/openmicroscopy/incubator/omero-python-importer.

Finally, just in case it's of use for any of your users, the Java version of that library which both insight and the CLI use to import could be used from MATLAB if you wanted. See https://docs.openmicroscopy.org/omero/5 ... brary.html for links to details.

All the best,
~Josh