OMERO.figure and multiple ROIs

Hi, I ran into an issue today in OMERO. I have images that have large numbers of ROIS (in the thousands). I am trying to use one of the later ROIs to generate a figure. OMERO.figure does not consider that there might be a large number of ROIs in an image and only looks at the first 200 results as far as I can tell (See Documentation found here JSON API — OMERO 5.6.2 documentation). When I ask to add a specific ROI in the add image option I am told that ROI cannot be found. Is there a way around this? This will be an ongoing issue for my group. We will routinely generate many ROIs and then want to select isolated examples to pull into figures. Thanks for the help!

Just to add a bit of extra context to this (I’m working with Susan on this issue): specifically on the “crop” functionality, OMERO.figure doesn’t seem to be handling pagination when retrieving ROIs using the JSON API.

I have done some testing on our (dev) web server, and when omero.web.api.limit was the default value of 200, rectangular ROIs inside the first 200 showed up as crop options, while the ones beyond 200 didn’t. Bumping omero.web.api.limit to 300 showed the ones between 200 and 300 as well, as expected.

Thanks for the feedback. You are right that OMERO.figure doesn’t support pagination of ROIs, either in the Edit ROIs dialog, when adding various Lines, Polygons, Ellipses & Rectangles from OMERO, or in the Crop dialog when loading Rectangles.

This is a known issue, at least for the ROI dialog (see Handle >1k ROIs · Issue #334 · ome/omero-figure · GitHub) and I’ll note there that it’s also an issue in the Crop dialog too.

Adding a “Load More…” button to support pagination (or maybe even page number 1, 2, 3… buttons) wouldn’t be too much work. But I wonder how easy it is to find the Rectangle you want amongst hundreds of them? Are you able to distinguish the one you want by scrolling through the thumbnails alone?

Thanks for the feedback,


In this case, It is easy to identify the ROIs for the figure as they are the only rectangle ROIs are other are have a round (circular or elliptical ) shape so picking out the ROIs for the figure is easy. Also, in the future, If we did have ROIs with similar shape profiles, then we would likely be choosing ROIs based on Image feature information and would have specific ROI ID numbers we would be selecting for a figure. SO an option to add and ROI by number would work for us, as similar to how you can add additional Images by Image ID.

OK, great. If there are a smaller number of Rectangles on the Image, then the latest changes I’m proposing at Rois pagination by will-moore · Pull Request #422 · ome/omero-figure · GitHub would work well, since the crop dialog will only load Rectangles and ignore other ROIs. Finding a Rectangle based on ID can probably be left for when there’s a need. Feel free to let us know if/when you need this feature.

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The fix was included in today’s release: omero-figure/ at e0f19d8c38ae3cfc9248f632df285fd4e0b6f2cb · ome/omero-figure · GitHub

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