[ome-devel] BF exporter create big ome.tif file

[Yellen, Gary]

Hi Mary -
I previously had a similar problem using the bioformats code to export OME-Tiff’s - the files were oversized and the write time was extremely long. I’m still not sure of all the reasons for this, but it might help you to look at an earlier thread ([ome-devel] OME-Tiff writing using LOCI calls from MATLAB, and ModuloAlongT annotation).

In the message http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2014-October/003036.html, I attached my substitute MATLAB code which uses LOCI calls to construct the metadata, but which writes the actual Tiff file using the MATLAB Tiff() class.  The code won’t be directly applicable, but you can see my approach and I bet it will address your problem.  I achieved about a 50x improvement in writing speed, and a 3-fold improvement in file size. Sebastien later suggested that the filesize issue might be related to division of the images into strips, but I still never achieved similar speed with the bioformats calls.

Good luck,
Gary



On Jan 27, 2015, at 4:56 AM, Hadrien Mary <hadrien.mary at gmail.com<mailto:hadrien.mary at gmail.com>> wrote:

Hi,

I have an OME TIFF file (generated by Micro-Manager). It's original
size is 29.6MB. Now if I use BF exporter to save it, the created file
is exactly the same (dimensions and OME XML string) but the size is
really huge (654.8MB).

The file can be found here:
https://arwen.hadim.fr/public.php?service=files&t=80e1586f55c8795c0c1c86e96aac7281

This issue happens with other files as well.

Thanks

--
Hadrien Mary

Ph.D student in Biology
Tournier-Gachet Team
CNRS - LBCMCP - UMR 5088

Université de Toulouse - Bât. 4R3B1
118, route de Narbonne - 31062 Toulouse
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