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<div>Hi Kai</div>
<div><br>
</div>
<div>I have prepared a template script that we will include in our training material after review. <a href="https://github.com/ome/training-scripts/pull/16">https://github.com/ome/training-scripts/pull/16</a></div>
<div>The script:</div>
<div>* iterates through an OMERO Dataset</div>
<div>* opens each OMERO Image with the method allowing you to specify the plane you want to open</div>
<div>* load the OMERO ROIs associated to the Image.</div>
<div>* converts the ROIs and add them to the ROI manager</div>
<div>* section where you will run your macro is commented out. You can inject your macro</div>
<div><br>
</div>
<div>This script does not contain any code to save the output of the macro.</div>
<div><br>
</div>
<div>I think that we have migrated all the example scripts to the new repository. It will be preferable to use those ones.</div>
<div>Balaji has moved to a new position in Oxford few months ago</div>
<div>so the scripts on his private branch are not tested/used and might no longer work</div>
<div><br>
</div>
<div>Hope it helps</div>
<div><br>
</div>
<div>See you next week</div>
<div><br>
</div>
<div>Jmarie</div>
<div><br>
</div>
<div><br>
</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, 25 May 2018 at 17:02<br>
<span style="font-weight:bold">To: </span>jmarie burel <<a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>>, OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.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 again for your reply! I realise that my request was not very clear:<br>
</p>
<p>I have time laps images (hyperstacks of 2C,75Z, 150T) in OMERO which all have ROIs stored in only the first time point. The ROIs where added using OMERO.<br>
</p>
<p>I am trying to write a script that <br>
</p>
<p>(i) fetches the first time point from all hyperstacks of a given dataset including their ROIs (ie, per hyperstack 2C,75Z, 1T)<br>
</p>
<p>(iii) runs an ImageJ macro on each hyperstack. This macro will require the ROIs to be present in the ImageJ ROI manager<br>
</p>
<p>My current script is based on the old one from Balaji [1] and already achieves this in principle, but I can not limit the import to only the first time point.</p>
<p>With the newer version [2] you referred me to this can be fixed, but here I failed to import the ROIs from OMERO into the ImageJ ROI manager.</p>
<p>Is there maybe a neat way of how I could achieve my goal?<br>
Perhaps these two scripts could be combine (maybe including [3]?), but so far I failed to do so.</p>
<p>Thank you again for your help and see you soon at the meeting,<br>
Kai</p>
<p>[1] <a class="moz-txt-link-freetext" href="https://github.com/bramalingam/Omero-Imagej-Scripts/blob/master/omero_batch_analysis.py">
https://github.com/bramalingam/Omero-Imagej-Scripts/blob/master/omero_batch_analysis.py</a><br>
[2] <span id="OLK_SRC_BODY_SECTION"><a href="https://github.com/ome/training-scripts/blob/master/practical/jython/analyse_particles_from_dataset.jy">https://github.com/ome/training-scripts/blob/master/practical/jython/analyse_particles_from_dataset.jy<br>
[3] </a></span><a href="https://github.com/ome/training-scripts/blob/master/practical/jython/analyse_particles_from_dataset.jy"><span id="OLK_SRC_BODY_SECTION"></span></a><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>
<span id="OLK_SRC_BODY_SECTION"></span></p>
<br>
<div class="moz-cite-prefix">On 05/21/2018 02:17 PM, Jean-Marie Burel (Staff) wrote:<br>
</div>
<blockquote type="cite" cite="mid:D728756F.76782%25j.burel@dundee.ac.uk">
<div>Hi Kai</div>
<div><br>
</div>
<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" moz-do-not-send="true">https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/util/ROIHandler.java</a></div>
<div><br>
</div>
<div>This can be a bit confusing</div>
<div>Will you need a Jython script that convert imagej ROIs to OMERO?</div>
<div><br>
</div>
<div>Cheers</div>
<div><br>
</div>
<div>Jmarie</div>
<div><br>
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<span style="font-weight:bold">From: </span>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">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" moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a>>, jmarie burel <<a href="mailto:j.burel@dundee.ac.uk" moz-do-not-send="true">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" moz-do-not-send="true">
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>
<br>
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>
<br>
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>
<br>
Thanks and cheers,<br>
Kai<br>
<br>
<div class="moz-cite-prefix">On 05/17/2018 10:11 PM, Jean-Marie Burel (Staff) wrote:<br>
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<blockquote type="cite" cite="mid:D7239E31.7660E%25j.burel@dundee.ac.uk">
<div>Hi Kai</div>
<div><br>
</div>
<div><br>
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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>
<div><br>
</div>
<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>
<div><br>
</div>
<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>
<div><br>
</div>
<div>Cheers</div>
<div>Jmarie</div>
<div><br>
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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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