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

[Hadrien Mary]

Thank you both for the answer.

It's weird because the filesize is correct if I use bfconvert (coming
from OME 5.1.0-m1, 3 October 2014). But I just reinstalled Fiji and
enable BF update site but I still have an oversized file using BF
exporter... I didn't check any options when exporting (single file and
uncompressed).

Are you sure your BF version in Fiji is 5.0 and not 5.1 ? Version
provided by BF update site is 5.0.6-DEV.

--
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


On Tue, Jan 27, 2015 at 3:01 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
> Hi Hadrien,
>
>> 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).
>
> I cannot reproduce this problem with the latest version of Bio-Formats from
> the Bio-Formats update site.
>
> I tried saving your file using the Bio-Formats Exporter, as well as
> "converting" it to another OME-TIFF using the bfconvert command line tool.
> Here are my results:
>
> 29592020 test.ome.tif
> 29560221 bf-exporter.ome.tif
> 29558724 bfconvert.ome.tif
>
> The bfconvert used was a 2014-Dec-5 build of the develop branch. The
> Bio-Formats version in ImageJ was updated from the BF update site within the
> past few days.
>
> Is your installation fully up to date? Which options did you have checked
> when exporting? Etc.
>
> Regards,
> Curtis
>
> On Tue, Jan 27, 2015 at 10:56 AM, Hadrien Mary <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
>> _______________________________________________
>> ome-devel mailing list
>> ome-devel at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
>
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>