Open Microscopy Environment

Hello,

This post is a duplicate of https://github.com/openmicroscopy/biofo ... ssues/2366.
I do not know where I should post. Here or on the issue tracker of GitHub ?

I have been trying to convert to TIFF numerous SVS files with bfconvert.
They all seem corrupted.

Here is the result (opened with GIMP) of the conversion of http://openslide.cs.cmu.edu/download/op ... 3003-1.svs:



Here is the command line I have been using:

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.../bfconvert -bigtiff -series 0 ".../JP2K-33003-1.svs" ".../%z.%t.%c.tiff"

I am using latest bftools on Mac OS X 10.11 (but same thing is happening on Ubuntu 14.04):

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felixveysseyre$ ./bfconvert -version
Version: 5.1.9
VCS revision: c3065feb775a7a8c0cc2cf6e35979331cca2418b
Build date: 15 April 2016

Thanks for your help !

Dear Felix,

I have tried to reproduce your bug with the information you provided using some of our sample SVS files. Unfortunately, I've not been able to do so with either 5.1 or our current development version. It may be that the metadata or pixel data in our SVS files differs from yours.

Edit: Sorry, I didn't notice the link to the original file; I'll test with that.

Kind regards,
Roger

Dear Felix,

I was able to reproduce the problem with your image and 5.1.9, but it was working fine for me with the current 5.2 development milestone. It looks like there is a fix which needs backporting to 5.1: https://github.com/openmicroscopy/bioformats/pull/2168

If you would like to build Bio-Formats from git (dev_5_1 with the four commits in the above PR cherry-picked), this should give you a working version. http://www.openmicroscopy.org/site/supp ... rmats.html has some instructions; "ant jars tools" should be sufficient.


Kind regards,
Roger

Dear Felix,

I backported this and opened https://github.com/openmicroscopy/bioformats/pull/2371 for the next 5.1 release. If you want to build this, that will save the cherry-picking mentioned in the previous message.


Regards,
Roger

Thanks for your help !

I have been able to compiled the branch associated to your pull request.

The conversion from SVS to TIFF seems to work correctly now.

Do you know when the next 5.1 version will be released ?

Best regards,
Félix

Hi Félix,

thanks for the testing update. In addition to the fix backported by Roger, we are also investigated a logging regression. Once addressed, we are considering a Bio-Formats 5.1.10 release which would resolve these two issues.

Best,
Sebastien

Hi Sebastien,

Thanks for all the info !

I downloaded 5.1.10 version and tested it. Everything seems to work correctly.

Best regards,
Félix

Hi Félix,

thanks for letting us know. Glad to hear the 5.1.10 release was useful.

Best,
Sebastien