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<div>Hi Kai</div>
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<div>To read the ROI when opening an image from OMERO to ImageJ</div>
<div>We use the Bio-Formats Importer option</div>
<div>The ROIs are read using <a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/util/ROIHandler.java">https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/util/ROIHandler.java</a></div>
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<div>This can be a bit confusing</div>
<div>Will you need a Jython script that convert imagej ROIs to OMERO?</div>
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<div>Cheers</div>
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<div>Jmarie</div>
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<span style="font-weight:bold">From: </span>Kai Schleicher <<a href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a>><br>
<span style="font-weight:bold">Date: </span>Friday, 18 May 2018 at 16:33<br>
<span style="font-weight:bold">To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>>, jmarie burel <<a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-users] syntax for scripting the windowless importer in Jython<br>
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<p>Hi Jean-Marie,</p>
<p>thanks for your reply and the updated scripts! I switched to the newer version you mentioned and it works like a charm, it was easy to adept to fetch only the time points that I like to have!</p>
<p>I would like to further extend it and get the ROIs associated to that image from OMERO into the ROI manger of ImageJ.</p>
<p>I found how this could be done in the example scripts, i.e <a class="moz-txt-link-freetext" href="https://github.com/ome/training-scripts/blob/master/practical/jython/omero_rois_to_imagej_roi.jy">
https://github.com/ome/training-scripts/blob/master/practical/jython/omero_rois_to_imagej_roi.jy</a><br>
</p>
Just as a question, is this script already available as a class in OMER.insight?<br>
Like a "ROIwriter class", as opposed to the ROIreader class from org.openmicroscopy.shoola.util.roi.io<br>
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Since this is a feature that is already in OMERO.insight, I figure there must be such a class, I just don't know its name :)<br>
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I apologize in advance, as these type of questions must be tedious to answer one by one (you are not a class/command/package lookup service), but I just started trying to find my way through the documentation.<br>
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Thanks and cheers,<br>
Kai<br>
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<div class="moz-cite-prefix">On 05/17/2018 10:11 PM, Jean-Marie Burel (Staff) wrote:<br>
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<div>Hi Kai</div>
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<div>All the scripts are now available at <a href="https://github.com/ome/training-scripts" moz-do-not-send="true">https://github.com/ome/training-scripts</a></div>
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<div>I did a bit of digging and it seems that the option specifyRanges=true is taken into account only when windowless=false</div>
<div>In that case the values in the range dialog are read.</div>
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<div>We have written a new version of the script you mentioned</div>
<div>The new version does not use the BF-importer plugin</div>
<div><a href="https://github.com/ome/training-scripts/blob/master/practical/jython/analyse_particles_from_dataset.jy" moz-do-not-send="true">https://github.com/ome/training-scripts/blob/master/practical/jython/analyse_particles_from_dataset.jy</a></div>
<div>This should hopefully allow you to only retrieve the planes you want</div>
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<div>Cheers</div>
<div>Jmarie</div>
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<span style="font-weight:bold">From: </span>ome-users <<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" moz-do-not-send="true">ome-users-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Kai Schleicher <<a href="mailto:kai.schleicher@unibas.ch" moz-do-not-send="true">kai.schleicher@unibas.ch</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Thursday, 17 May 2018 at 18:11<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:ome-users@lists.openmicroscopy.org.uk" moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a>" <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>[ome-users] syntax for scripting the windowless importer in Jython<br>
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<p>Dear OME-team,</p>
<p>To script the windowless BF-importer in Jython I am building on the cool <a moz-do-not-send="true" href="https://github.com/bramalingam/Omero-Imagej-Scripts/blob/master/omero_batch_analysis.py">
script by Balaji</a>.</p>
<p>I specifically wish to limit the import to the first time-point of my datasets, but I am struggling at getting the syntax right.</p>
<p>In IJ1-macro language it works like this:<br>
</p>
<blockquote type="cite">run("Bio-Formats Importer", "open=V:/small5Dstack.tif specify_range t_begin=1 t_end=1 t_step=1");</blockquote>
In the jython script I tried to add a line 53:<br>
<blockquote type="cite">options += " specifyranges=true tbegin=1 tend=1 tstep=1 "</blockquote>
But it still loads the entire dataset.<br>
I tried a few other strings without luck and was wondering if you could maybe just point me to the proper way of doing it.
<p>Thanks and see you soon at the meeting,<br>
Kai</p>
<pre class="moz-signature" cols="72">--
>>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) | <a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch" moz-do-not-send="true">kai.schleicher@unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch" moz-do-not-send="true">www.biozentrum.unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch" moz-do-not-send="true">www.microscopynetwork.unibas.ch</a></pre>
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