Open Microscopy Environment

Hi all,

Is it currently possible to export the vertices of a polygon ROI to a spreadsheet?

So far I have tried selecting "Coord List(X)" and "Coord List(Y)" using the "Results Wizard..." in the ROI tool, then using "Save to Excel...", but I get an error message saying "Cannot save the ROI results". This doesn't occur when I try to save other measurements such as the centre coordinates.

Interestingly the error seems to be specific to "Coord List(Y)". If I only select "Coord List(X)" the save completes without error, but the corresponding column in the generated spreadsheet is empty. I could upload the image if it would be helpful (I'm not sure how to export the ROIs themselves).

Alistair

Hi Alistair,

which version of Insight do you use? And is it possible got get the log file (Help -> Show Log File)? You can upload it here: https://www.openmicroscopy.org/qa2/qa/upload/

I tried to replicate the error with the latest version 5.2.2. I didn't get an error, but there's definitely something wrong with "Coord List(X)" and "Coord List(Y)" export of polygons, both are empty in the Results table, but in the exported Excel file values for "Coord List(Y)" are there, but still "Coord List(X)" is empty. I continue investigating the issue, but still it would be good to see the detailed error log you got.

Regards,
Dominik

Hi Dominik, thanks for your reply.

which version of Insight do you use?

I'm also using 5.2.2.

And is it possible got get the log file (Help -> Show Log File)?

I've uploaded the whole log file here. Here's what happens when I attempt to export both X and Y coordinate lists:

Code: Select all

2016-04-14 12:40:57,073 INFO  [   o.o.s.env.data.login.LoginServiceImpl] (nitializer) Logged onto OMERO at: cjagpu3.pharm.ox.ac.uk
User Name: alistair -- Password: ********

2016-04-14 12:40:58,359 WARN  [     o.o.s.a.m.editor.AnnotationTaskPane] (nitializer) UI for displaying ROIS annotations not implemented yet!
2016-04-14 12:40:58,748 DEBUG [       omero.gateway.facility.Facility$1] ( Thread-12) Created new BrowseFacility
2016-04-14 12:41:04,319 DEBUG [       omero.gateway.facility.Facility$1] ( Thread-26) Created new ROIFacility
2016-04-14 12:41:04,321 DEBUG [       omero.gateway.facility.Facility$1] ( Thread-26) Created new DataManagerFacility
2016-04-14 12:41:06,503 WARN  [     o.o.s.a.m.editor.AnnotationTaskPane] (entQueue-0) UI for displaying ROIS annotations not implemented yet!
2016-04-14 12:41:12,278 ERROR [      o.o.s.a.m.view.MeasurementViewerUI] (entQueue-0) Problem while handling ROI No ROIShape on coord T: 0 Z: 0
2016-04-14 12:41:35,284 WARN  [     o.o.s.a.m.editor.AnnotationTaskPane] (entQueue-0) UI for displaying ROIS annotations not implemented yet!
2016-04-14 12:41:38,683 ERROR [      o.o.s.a.m.view.MeasurementViewerUI] (entQueue-0) Problem while handling ROI No ROIShape on coord T: 0 Z: 0
2016-04-14 12:41:51,478 WARN  [     o.o.s.a.m.editor.AnnotationTaskPane] (entQueue-0) UI for displaying ROIS annotations not implemented yet!
2016-04-14 12:43:21,581 ERROR [       o.o.s.a.m.view.MeasurementResults] (entQueue-0) Cannot save the results null


Thanks for uploading the log. I'll keep you posted when I fixed the problem. Hope I'll get it in for the next release 5.2.3.

Regards,
Dominik