Direct export to OMERO

[PhilippeP]

Hi there,

I am new here, so forgive me if my question is "inappropriate". I did a search on the FAQ, as well as on this forum, and was surprised to find nothing... Maybe I miss something?

Isn't it possible to directly export images to OMERO during acquisition? That would save us a lot of time, avoid many potential mistakes while subsequently exporting (we are doing HCS, with thousands of images at each session), not talking about the files regularly abandoned on the microscope PC...

[jmoore]

Hi Philippe,

Isn't it possible to directly export images to OMERO during acquisition?

It's certainly possible but very much depends on your setup. What acquisition system/software are you using? Have you written it yourself? In what language?

In our terminology, this would likely be considered a customer importer. In Java, there's an ImportLibrary helper to make this easier, but others have written similar custom importers in C++ and Python.

What version of OMERO are you currently using?

Cheers,
~Josh

[PhilippeP]

Thank you for your feedback!
I am not running anything yet, more on a "just looking" approach.
I guess we will set up the last OMERO version? We are using a Zeiss station, with their Zen software.

[jmoore]

Hi Philippe,

I guess we will set up the last OMERO version?

The latest stable version is 4.4.9, and that would certainly be a good place to start. Acquiring directly into OMERO will require the use of the API for which something like Zen OAD would be useful.

The latest develop version is 5, currently beta1. Beta2 will hopefully come out towards the end of this year, and may include a second option for you: "in-place import". I've just a filed https://trac.openmicroscopy.org.uk/ome/ticket/11573 for tracking this work. Please let me know if you would like to be CC'd.

Cheers,
~Josh