Hi -
I have found that adding an image annotation (in this case a ModuloAlongT annotation) interferes with subsequent function of setLightPathDichroicRef and setLightPathEmissionFilterRef, not only for the annotated image series but for subsequent series.
It works fine if I first do the setLightPathEmissionFilterRef, etc., and put off the call to OMEXMLService.addModuloAlong(metadata, coreMetadata, series);
until all other metadata are written.
Thanks - gary