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

[Kai Schleicher]

Hi Petr,

awesome - thanks! Problem solved :)

Have a nice evening and cheers,
Kai


On 04/25/2018 04:43 PM, Petr Walczysko (Staff) wrote:
> 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
>
>      _______________________________________________
>      ome-users mailing list
>      ome-users at lists.openmicroscopy.org.uk
>      http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096

-- 
>> 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