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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Will,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Sure, that would be nice. Select a screen plate (in a dropdown) and then select wells, maybe I only want half the plate or 1 well or the whole plate.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">After that, a batch export would occur, creating say 1 OME-TIF per Field (since you can have more than 1 Field) per Well.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">It should obviously not kill the Server, however at least from our side, we will have a relatively strong infrastructure.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Is there anything known on a timeframe or anything we can do to help ?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">--<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Christophe<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#7F7F7F">................................................................................<o:p></o:p></span></b></p>
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<b><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:gray">Dipl.-Ing. Christophe TREFOIS</span></b><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#7F7F7F"><br>
</span><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:gray">PhD Student<o:p></o:p></span></p>
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<i><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:gray">Ing. Sys. Com. Dipl. EPF<o:p></o:p></span></i></p>
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<span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:gray"><br>
<img width="37" height="38" id="Picture_x0020_1" src="cid:image001.jpg@01CC5203.5D6C2610" alt="Description: cid:image001.jpg@01CACC35.07191DE0"><o:p></o:p></span></p>
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<span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:gray">Luxembourg Centre for Systems Biomedicine<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:3.0pt"><span style="font-size:8.0pt;font-family:"Calibri","sans-serif";color:gray">UNIVERSITY OF LUXEMBOURG</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:gray"><br>
</span><span style="font-size:8.0pt;font-family:"Calibri","sans-serif";color:gray">CAMPUS LIMPERTSBERG<br>
162a, avenue de la Faïencerie<br>
L-1511 Luxembourg<o:p></o:p></span></p>
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<span style="font-size:8.0pt;font-family:"Calibri","sans-serif";color:gray">T +352 46 66 44 6124<br>
F +352 46 66 44 6949<br>
</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><a href="http://www.uni.lu/" title="blocked::http://www.uni.lu/
http://www.uni.lu/"><span style="font-size:8.0pt;color:gray">www.lcsb.lu</span></a></span><span style="font-size:8.0pt;font-family:"Calibri","sans-serif";color:#7F7F7F"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Will Moore [mailto:will@lifesci.dundee.ac.uk]
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<b>Sent:</b> Wednesday, August 03, 2011 5:09 PM<br>
<b>To:</b> Christophe TREFOIS<br>
<b>Cc:</b> ome-users@lists.openmicroscopy.org.uk<br>
<b>Subject:</b> Re: [ome-users] OME-TIF Batch Export<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Christophe,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The limitation on exporting OME-TIFF is really just the processing required on the server to generate the files, since this requires a lot of database traversing and moving data around. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">We are currently experimenting with adding OME-TIFF support to the Batch_Image_Export script.<o:p></o:p></p>
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<p class="MsoNormal">This should address the functionality you want, but it will need some assessment to see how the server holds up when batch exporting large numbers of images. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The other issue is that the script currently runs on Datasets of images (or Images identified by ID), but you'd presumably want to specify a Plate of Images?<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> Will.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 3 Aug 2011, at 16:00, Christophe TREFOIS wrote:<o:p></o:p></p>
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<br>
<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">Dear Ome’s (is that correct?),<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">I read on some forums that there is no batch export for OME-TIF and I also only found a batch export for PNG or JPG.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">Is there a specific reason for that?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">More specifically, does anyone of you have any experience with this?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">We would like to use OMERO with HCS data (Opera). Mass Import AND Export therefor becomes a necessity.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">Thanks for any help,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">--<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black">Christophe<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:#7F7F7F">................................................................................</span></b><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:3.0pt"><b><span style="font-size:10.0pt;color:gray">Dipl.-Ing. Christophe TREFOIS</span></b><span style="font-size:9.0pt;color:#7F7F7F"><br>
</span><span style="font-size:9.0pt;color:gray">PhD Student</span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:3.0pt"><i><span style="font-size:9.0pt;color:gray">Ing. Sys. Com. Dipl. EPF</span></i><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;margin-bottom:3.0pt"><span style="font-size:9.0pt;color:gray"><br>
<image001.jpg></span><span style="color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:6.0pt"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:gray">Luxembourg Centre for Systems Biomedicine</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:3.0pt"><span style="font-size:8.0pt;font-family:"Calibri","sans-serif";color:gray">UNIVERSITY OF LUXEMBOURG</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:gray"><br>
</span><span style="font-size:8.0pt;font-family:"Calibri","sans-serif";color:gray">CAMPUS LIMPERTSBERG<br>
162a, avenue de la Faïencerie<br>
L-1511 Luxembourg</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"><o:p></o:p></span></p>
<p class="MsoNormal" style="margin-bottom:3.0pt"><span style="font-size:8.0pt;font-family:"Calibri","sans-serif";color:gray">T +352 46 66 44 6124<br>
F +352 46 66 44 6949<br>
</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"><a href="http://www.uni.lu/" title="blocked::http://www.uni.lu/ http://www.uni.lu/"><span style="font-size:8.0pt;color:gray">www.lcsb.lu</span></a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black">_______________________________________________<br>
ome-users mailing list<br>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black">William Moore<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black">Wellcome Trust Centre for Gene Regulation & Expression<o:p></o:p></span></p>
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