Failed uploading all the ORBIT segmented object to OMERO

Here the issue:

i have run a model in ORBIT and obtained some objects from segmentation

then i have created the ROI in ORBIT and run the model to the entire image.
I followed the instructions for adding the objects to OMERO and in this image you can see in pink the annotation polygon boundaries i have created.

i run the script provided here (changed username and password)

and this is the message i get

When i check the ROI in OMERO i found only 10 which is not the entire number i should have (see green spots in the first image)

Anyone knows why only a handful of segmented objects has been uploaded?

Thanks a lot!

Hi @Ilaria,

the script tries to use the currently opened image in Orbit, but it seems not to find one (“found 0 files” in the log).
Do you have an open image in Orbit when executing the script?


@mstritt yes the same image i used for running the model is opened in Orbit and of course OMERO is running as the image comes from OMERO and not from a local folder.

I see the point. Can you

  1. store your segmentation model in orbit (/Omero) via model -> save on server.
    Then open the “load model from server” dialog and note the model id.

  2. Then, replace this paragraph

// Load Models that I own. OMERO annotations of type: Model
List<RawAnnotation> annotations = imageProvider.LoadRawAnnotationsByType(RawAnnotation.ANNOTATION_TYPE_MODEL)
println("Found " + annotations.size() + " files")
// Use the first annotation
int fileAnnId = annotations[0].getRawAnnotationId()
OrbitModel model = OrbitModel.LoadFromOrbit(fileAnnId)
println("Loaded Model: " + model.getName())

with simply this

OrbitModel model = OrbitModel.LoadFromOrbit(<MODEL-ID>)
println("Loaded Model: " + model.getName())

(replace with your model id.

Then it should work.


@mstritt unfortunately it didn’t work and this time i have a different error message

see part a) and b) here

Note that i am the owner of that image in omero


so i am actually puzzled on that “security violation message”

the model when saved appears like this

ELB droneimages is actually the name of the dataset and not the image as showed below


any clue of why i get that violation message? is an issue with OMERO or there is something more we need to add to the script?

Thanks a lot

Is the Image in your default group in OMERO? If you log out of webclient and log in again, do you enter the group that contains your Image (and the Orbit model)?
If not, then the script needs to do more work to switch the group context, and we can help with that if that’s the issue. (that would also explain why it didn’t find the Orbit model in the first time).

A short-term workaround might be to switch your default group in the webclient to match the group that the image is in. Look under “User Settings” in the menu at the top-right of the page.


1 Like

@will-more thanks a million. Issue sorted. You were right, the image wasn’t in the default group of the user. However, by changing it in OMERO, the model was read perfectly and the ROIs were created matching the segmented objects.
I will keep in mind this for other similar cases.