[ome-users] MetaXpress image has cropped metadata values (with fix)

[Sebastien Besson]

Dear Mario,

this looks like the same underlying issue as the one you reported a month ago in
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2015-February/005037.html

Roger had opened a Pull Request to fix this bug and this change got merged into the 5.1
development line - see https://github.com/openmicroscopy/bioformats/pull/1584.

I retested the sample file you sent using the last development milestone of Bio-Formats 5.1.x
http://downloads.openmicroscopy.org/bio-formats/5.1.0-m4/ and the metadata should be correctly
read by the upcoming 5.1.0 release of Bio-Formats:

$ ./bftools/showinf -version
Version: 5.1.0-m4
VCS revision: 51bf71d
Build date: 19 February 2015
$ ./bftools/showinf b0BCDSL-T069_wG06_s6_z0_t1_cCy5_u001.tif | grep Experiment
Experiment base name: SL-HeLa4channels
Experiment set: SL-HeLa4channels

Best regards,
Sebastien

> On 20 Mar 2015, at 10:55, Mario Emmenlauer <mario at emmenlauer.de> wrote:
> 
> 
> Dear Bio-Formats developers,
> 
> I have a small issue with MetaXpress meta data. When I read the image
> (link below), several metadata values are missing their first character.
> An example is 'Experiment base name' for which I expect to get
> 'SL-HeLa4channels', instead I receive 'L-HeLa4channels'. I could identify
> in components/formats-gpl/src/loci/formats/in/MetamorphReader.java the
> code expects always a dummy character after the colon, however in my case
> I think this dummy is missing. Here a proposed fix:
> 
> -          String value = line.substring(colon + 2);
> +          // Mario Emmenlauer, 2015.03.20: There is not always a space after
> +          // the colon, so better use 'trim()' instead of expecting a space:
> +          String value = line.substring(colon + 1).trim();
> 
> I did not extensively check this fix, so maybe use it with a bit of
> caution. The image I used is here:
>    http://data.marssoft.de/b0BCDSL-T069_wG06_s6_z0_t1_cCy5_u001.tif
> 
> All the best, and thanks for your great work,
> 
>     Mario Emmenlauer
> 
> 
> 
> 
> 
> 
> -- 
> Mario Emmenlauer BioDataAnalysis             Mobil: +49-(0)151-68108489
> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
> D-81669 München                          http://www.marioemmenlauer.de/
> 
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