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Hi Kai,
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<div class="">The method you were using was indeed correct as was your suspicion that the contents of the CellH5 file were being overwritten.</div>
<div class="">I was able to reproduce similar behaviour and from debugging it appears this a bug in the CellH5Writer when dealing with multi series data.</div>
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<div class="">I have opened a bug ticket below which can be used to track this issue:</div>
<div class=""><a href="https://trac.openmicroscopy.org/ome/ticket/13327#ticket" class="">https://trac.openmicroscopy.org/ome/ticket/13327#ticket</a></div>
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<div class="">With Thanks,</div>
<div class="">David Gault</div>
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<blockquote type="cite" class="">
<div class="">On 27 Mar 2017, at 16:32, Kai Schleicher <<a href="mailto:kai.schleicher@unibas.ch" class="">kai.schleicher@unibas.ch</a>> wrote:</div>
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<div bgcolor="#FFFFFF" text="#000000" class="">Hi ,<br class="">
<br class="">
I have a question grading the HCS data format cellH5. Basically, I think it looks really promising and I'd be happy to try it out - of course on our OMERO! :D<br class="">
<br class="">
One of our current projects deals with HCS data obtained in the *.HTD format (<a moz-do-not-send="true" href="https://filesender.switch.ch/filesender/?vid=00488c80-0325-e308-fafe-000008cef24f" class="">download</a>, 14 GB).<br class="">
<br class="">
>From what I have <a href="http://www.cellh5.org/" class="">read</a>, the cellh5 format should be vastly superior to this and I also noticed that
<a href="http://www.openmicroscopy.org/site/support/bio-formats5.4/formats/cellh5.html" class="">
Bio-formats can read and write *.ch5 image files</a>.<br class="">
<br class="">
Hence my (probably very naive) question: Would you know of a method to convert our *.HTD dataset to *.ch5?<br class="">
<br class="">
I have tried something very simple using the <a moz-do-not-send="true" href="http://www.openmicroscopy.org/site/support/bio-formats5.4/users/comlinetools/" class="">
bio-formats command line tools</a>, which almost worked (see below) :)<br class="">
<br class="">
I saw the console iterate through every image, but the resulting *.ch5 however contained only a single position/image.<br class="">
<br class="">
My suspicion is that all tiffs contained in the *.HTD where written to the exact same place in the *.ch5 file, i.e. where overwritten constantly.<br class="">
<br class="">
Thank you very much for your help!<br class="">
<br class="">
With best greetings from Basel,<br class="">
Kai<br class="">
<br class="">
---<br class="">
code for windows<br class="">
<blockquote type="cite" class="">for %%i in (*.HTD) do C:\Tools\bftools\bfconvert %%i %%~ni.ch5</blockquote>
<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">kai.schleicher@unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch/">www.biozentrum.unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch/">www.microscopynetwork.unibas.ch</a></pre>
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