Open Microscopy Environment

Hi, all, I’m new to Omero. I have a situation where I’m accumulating a time series of tiff files: A_T1.tif, A_T2.tif, … , A_T9.tif. At some point during the accumulation, I have perhaps 3 of these files ready. I can successfully load these 3 files into Omero using a pattern file (A_T<1-3>.tif). Doing this, the data seems correctly grouped into the early part of my time series. Once A_T4.tif is ready, is there a way to create the now-longer series (A_T<1-4>.tif) without re-importing the first files?

Ideally, I would like to do this programmatically through Python, but any guidance on programmatic or interactive approaches would be appreciated.

I am afraid that OMERO import is designed as a one-time thing: it was never thought of as being incremental.

There might be tricks outside vanilla import that could work to add another plane to an imported image but they would require fairly advanced use of the Blitz API and/or manipulation of the related OMERO model objects and we doubt that we have yet thought of an approach that would surely work. As a new user please be reassured that you are certainly not missing anything obvious or easy about how this could be done.

Cheers,
Mark

Thanks for the response, Mark. Given that, we’ve worked around this issue by using ideas from the “Combine Images…” utility script, essentially combining the images after all the imports complete. That solution isn’t ideal but might suffice. We’ve also started using the *.ome.tiff format but only to combine our channels not to combine the time dimension.
Really, the only reason I want the images combined into a time-series is so I have a time slider in the viewer. To perhaps broaden my original question a little, is there any other solution that comes to mind to take images from individual timepoints and display them in a viewer with a time slider? In other words, can I make one of the viewers treat my images as a time-series (hyper-stack) without actually combining the image?
Thanks, MLB

I'm afraid this doesn't exist at the moment, but I've created a feature-request card for iviewer at
https://trello.com/c/n3i6a2RO/43-combin ... across-z-t

An alternative to to create a small OMERO.web Django app that only has your bare minimum functionality (using a slider to scroll between images). See https://docs.openmicroscopy.org/omero/5 ... teApp.html
The amount of code needed to do this would be pretty minimal (using default rendering settings), but you wouldn't have all the other functionality of OMERO.iviewer (tiling, ROI support, adjust rendering settings etc)
so it might not be the best idea unless this feature is critical for you.

Regards,

Will.