[ome-users] Convert HTD to Cellh5 using Bioformats

[David Gault (Staff)]

Hi Kai,

The method you were using was indeed correct as was your suspicion that the contents of the CellH5 file were being overwritten.
I was able to reproduce similar behaviour and from debugging it appears this a bug in the CellH5Writer when dealing with multi series data.

I have opened a bug ticket below which can be used to track this issue:
https://trac.openmicroscopy.org/ome/ticket/13327#ticket

With Thanks,
David Gault

On 27 Mar 2017, at 16:32, Kai Schleicher <kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch>> wrote:

Hi ,

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

One of our current projects deals with HCS data obtained in the *.HTD format (download<https://filesender.switch.ch/filesender/?vid=00488c80-0325-e308-fafe-000008cef24f>, 14 GB).

>From what I have read<http://www.cellh5.org/>, the cellh5 format should be vastly superior to this and I also noticed that Bio-formats can read and write *.ch5 image files<http://www.openmicroscopy.org/site/support/bio-formats5.4/formats/cellh5.html>.

Hence my (probably very naive) question: Would you know of a method to convert our *.HTD dataset to *.ch5?

I have tried something very simple using the bio-formats command line tools<http://www.openmicroscopy.org/site/support/bio-formats5.4/users/comlinetools/>, which almost worked  (see below) :)

I saw the console iterate through every image, but the resulting *.ch5 however contained only a single position/image.

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.

Thank you very much for your help!

With best greetings from Basel,
Kai

---
code for windows
for %%i in (*.HTD) do C:\Tools\bftools\bfconvert %%i %%~ni.ch5

--
>>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) | kai.schleicher at unibas.ch<mailto:kai.schleicher at unibas.ch> | www.biozentrum.unibas.ch<http://www.biozentrum.unibas.ch/> | www.microscopynetwork.unibas.ch<http://www.microscopynetwork.unibas.ch/>

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