Mixing OMERO & bio-formats from Matlab.

[i.munro]

Hi

I just managed to get Matlab code, which mixes OMERO & bio-formats, running deployed (i.e. compiled on the run-time engine rather than from source) on Win7.

On loading OMERO & bio-formats I get

Screen Shot 2014-05-15 at 21.08.56.png (35.17 KiB) Viewed 1681 times

Do I need to be concerned about this? I haven't found see any other symptoms yet.

I have yet to establish whether this also happens on OSX. It certainly doesn't running from source on OSX.

Regards

Ian

[sbesson]

Hi Ian,

yes the error makes sense as we provide slf4j-api as a standalone JAR in OMERO.matlab while it is bundled with bioformats_package.jar. So conflicting JARs are found at initialization. Assuming nothing goes wrong so far, this might not be a concern for you esp. since we use the same version of sl4j-api in both projects.

I think the proper way to avoid this conflict is to:
- either prevent loading the sl4f-api.jar shipped with OMERO.matlab
- or add indidivudal Bio-Formats JARs (formats-api.jar, formats-gpl.jar...) rather than the bioformats_package.jar bundle

A reasonable mid-term solution will certainly arise following Balaji's recent effort on importing images/plates from MATLAB. This means we may start bundling the Bio-Formats libraries as part of the libs/ directory of OMERO.matlab in the near future and we will likely solve this issue using one of the two options descriped above.

Sebastien

[i.munro]

Thanks Sebastien

Ian