[ome-users] BioFormat problem with some BioRad .1sc files

[Geert Meesen]

Great service :-)

To give you all an idea what I'm doing with ImageJ/Bio-Formats :

We have a BioRad Geldoc XR system (DNA gel imaging, molecular 
biotechnology lab).

Users save the images in .1sc format on a network disk on a Linux server 
under a folder with their E-mail address as name. This networkdisk is 
mounted on a Windows XP computer connected to the GelDoc system and is 
only accessible from that computer.

A perl script called iwatch (http://iwatch.sourceforge.net/) runs on the 
linux server and monitors activity under this folder. Once it detects a 
new file, it calls a custom script I wrote to convert the file to two 
jpeg files (one normal, one inverted) with the help of 
ImageJ/Bio-Formats in batch mode. These jpeg files and the original .1sc 
file are then mailed to the person the folder belongs too. This activity 
is also logged to a MySQL database.

I put this system in order since a couple of weeks and the users are 
very enthousiastic about it ;-)

Before, they had to save the image in .1sc format, then export them to 
.jpeg, using the software provided by BioRad (Quantity One) and then 
E-mail the files to themselves by logging in to their webmail accounts 
(or use a USB-stick, but I discouraged this option as it is more prone 
to computervirus-infections).

Thanks again :-)

Geert.

On 25/04/2012 21:35, Melissa Linkert wrote:
> Hi Geert,
>
>> I noticed a problem with the Bio-Formats library while reading
>> BioRad .1sc files (for the GelDoc system).
>>
>> Some files are misinterpreted and show the wrong result. Most files
>> however are correct.
>>
>> This is the setting :
>>
>> - BioFormat "Trunk build" from 20 april 2012
>> - ImageJ 1.46j (Fiji distribution)
>> - Java 1.6.0_24 (32 bit)
>> - Windows XP (32 bit)
>>
>> All files in full resolution can be found in this zip file =
>>
>> http://www.MolecularBiotechnology.UGent.be/files/biorad-1sc.zip
> Thank you very much for reporting this problem, and for providing all of
> the information necessary to duplicate and fix it.  We have just now
> implemented a fix, so the upcoming 4.4 release of Bio-Formats should
> open both .1sc files correctly.
>
> Regards,
> -Melissa
>
> On Mon, Apr 23, 2012 at 03:18:08PM +0200, Geert Meesen wrote:
>> Hi all,
>>
>> I noticed a problem with the Bio-Formats library while reading
>> BioRad .1sc files (for the GelDoc system).
>>
>> Some files are misinterpreted and show the wrong result. Most files
>> however are correct.
>>
>> This is the setting :
>>
>> - BioFormat "Trunk build" from 20 april 2012
>> - ImageJ 1.46j (Fiji distribution)
>> - Java 1.6.0_24 (32 bit)
>> - Windows XP (32 bit)
>>
>> All files in full resolution can be found in this zip file =
>>
>> http://www.MolecularBiotechnology.UGent.be/files/biorad-1sc.zip
>>
>> It contains the following files :
>>
>> - good example1.1sc = the original .1sc file showing an example that
>> imports ok in Bio-Formats
>>
>> - good example1.1sc.jpg = the jpeg version of the above file, saved
>> with ImageJ
>>
>> - bad example1.1sc = the original .1sc file showing an example that
>> imports bad in Bio-Formats
>>
>> - bad example1.1sc.jpg = the jpeg version of the above file, saved
>> with ImageJ
>>
>> - bad example1.jpg = the jpeg version of the .1sc file, saved by
>> "Quantity One" (the BioRad software).
>>
>> The imagesize is 1360 x 1024
>>
>> (as a quick guide, I added the "good" version and the "bad" version
>> of the "bad example" file to this E-mail in reduced format. The
>> full-size images are in the zip-file).
>>
>> The 2 BioRad files are taken with the same machine on the same
>> computer and most of the times the conversion is perfect. Just some
>> files give this error.
>>
>> I get the same result when running it on a Linux system.
>>
>>
>> Thanks in advance if anybody of you can shed a light on this error.
>>
>> Bye,
>>
>> Geert.
>>
>> -- 
>> Geert Meesen.
>> Infrastructure Manager.
>> Dep. Molecular Biotechnology, Ghent University
>> Coupure Links 653
>> B-9000 Gent, Belgium
>> ---------------------------------------------------
>> http://www.MolecularBiotechnology.UGent.be/
>> E.Mail : Geert.Meesen at UGent.be
>> Tel. : +32-9-264.59.68
>> Fax. : +32-9-264.62.19
>> E-Mail disclaimer : see http://www.ugent.be/e-maildisclaimer
>>
>
>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

-- 
Geert Meesen.
Infrastructure Manager.
Dep. Molecular Biotechnology, Ghent University
Coupure Links 653
B-9000 Gent, Belgium
---------------------------------------------------
http://www.MolecularBiotechnology.UGent.be/
E.Mail : Geert.Meesen at UGent.be
Tel. : +32-9-264.59.68
Fax. : +32-9-264.62.19
E-Mail disclaimer : see http://www.ugent.be/e-maildisclaimer