[ome-users] ImageJ-OMERO connector loses z-position of ROIs drawn in OMERO

[Petr Walczysko (Staff)]

Dear Kai

Would you please try for me the following:

In Fiji, in your ROI Manager:

  - click on More
  - click on Options
  - check the "Associate Show All ROIs with Slices" checkbox
  - close and re-open the image which you opened from OMERO
  - or if you did not connect yet, connect to OMERO, open the image from OMERO
  - click onto the ROIs which are loaded into the ROI Manager and observe that the viewer of the image in Fiji is jumping to the appropriate Z section

This at least works for me. Please let us know if that helps.

All the best

Petr

Petr Walczysko

OME Team




On 25/04/2018, 14:43, "ome-users on behalf of Kai Schleicher" <ome-users-bounces at lists.openmicroscopy.org.uk on behalf of kai.schleicher at unibas.ch> wrote:

    Dear OME-team,

    I have annotate an image (eg. ID 18394 on your demo server) with ROIs in
    different z-positions (here z=4 and 1) using OMERO.insight.

    I then open that image including its ROIs in FIJI using the current
    version of the ImageJ-OMERO connector.

    While the ROIs are present in Fijis ROI manager, their proper z-position
    is lost (see evaluation macro below).

    I seem to remember that this used to work, but right now I have no idea
    what changed. Could you help me out?

    Thanks and cheers,
    Kai

    // get the number of rois
    rnumbers = roiManager("count");
    print("number of Rois= "+rnumbers);

    // for each ROI: get and print z-position
    for (i=0; i<rnumbers; i++) {

         // select ROI
         roiManager("Select", i);

         // get the zposition that the ROI is in
         pos = eval("js","IJ.getImage().getRoi().getPosition()");
         print("position= "+pos);
    }


    --
    >>Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
    Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
    Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | kai.schleicher at unibas.ch | www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

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