Read OME metadata using SCIFIO

scifio-metadata.groovy

#@ ImageJ ij
#@ File file

import io.scif.config.SCIFIOConfig;
import io.scif.config.SCIFIOConfig.ImgMode;
import io.scif.ome.OMEMetadata

// Open and display a file as a cell image.
config = new SCIFIOConfig().imgOpenerSetImgModes(ImgMode.CELL)
dataset = ij.scifio().datasetIO().open(file.getAbsolutePath(), config)
ij.ui().show(dataset)

// Extract metadata from a file opened in this manner.
globalMeta = dataset.getProperties().get("scifio.metadata.global")
imageMeta = dataset.getProperties().get("scifio.metadata.image")

// --OR-- We can read _only_ the metadata from a file without opening pixels.
//globalMeta = ij.scifio().initializer().parseMetadata(file.getAbsolutePath())

// Convert globalMeta above to omeMeta
omeMeta = new OMEMetadata(ij.context())
ij.scifio().translator().translate(globalMeta, omeMeta, true)

// Access some metadata from the OME trove. The below
// is just a small example of what the OME API provides.
omexml = omeMeta.getRoot()
iCount = omexml.getInstrumentCount()
for (iIndex = 0; iIndex < iCount; iIndex++) {
	println("Instrument #" + iIndex + ":")
	println("\tID = " + omexml.getInstrumentID(iIndex))
	oCount = omexml.getObjectiveCount(iIndex)
	for (oIndex = 0; oIndex < oCount; oIndex++) {
		println("\tObjective #" + oIndex + ":")
		println("\t\tID = " + omexml.getObjectiveID(iIndex, oIndex))
		println("\t\tLensNA = " + omexml.getObjectiveLensNA(iIndex, oIndex))
		println("\t\tModel = " + omexml.getObjectiveModel(iIndex, oIndex))
		println("\t\tManufacturer = " + omexml.getObjectiveManufacturer(iIndex, oIndex))
	}
}

I also get a No supported format found when trying with an lsm file:

io.scif.FormatException: E:\[...]\image1.lsm: No supported format found.

For MSR files, this is because the SCIFIO OBFReader is taking precedence over Bio-Formats. But unfortunately, the SCIFIO OBFReader does not handle all MSR files successfully. The issue could be solved by addressing scifio/scifio-bf-compat#12.

I was not able to duplicate the LSM issue with the 2chZT.lsm sample from https://loci.wisc.edu/software/sample-data. Does this particular LSM file open successfully with Bio-Formats?