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Hi ,<br>
<br>
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>
<br>
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">download</a>,
14 GB).<br>
<br>
From what I have <a href="http://www.cellh5.org/">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">Bio-formats
can read and write *.ch5 image files</a>.<br>
<br>
Hence my (probably very naive) question: Would you know of a method
to convert our *.HTD dataset to *.ch5?<br>
<br>
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/">bio-formats
command line tools</a>, which almost worked (see below) :)<br>
<br>
I saw the console iterate through every image, but the resulting
*.ch5 however contained only a single position/image.<br>
<br>
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>
<br>
Thank you very much for your help!<br>
<br>
With best greetings from Basel,<br>
Kai<br>
<br>
---<br>
code for windows<br>
<blockquote type="cite">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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