Open Microscopy Environment

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



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

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

Thanks Sebastien

Ian