[ome-users] Convert HTD to Cellh5 using Bioformats

Kai Schleicher kai.schleicher at unibas.ch
Mon Mar 27 16:32:55 BST 2017

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 
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 

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 
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,

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 | www.biozentrum.unibas.ch | www.microscopynetwork.unibas.ch

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