I have a series of Olympus .oir files from a multi-area time lapse acquisition. One such file is:
I can use Python + bioformats to load this file and extract the image data. I can also start to see the associated metadata with this code:
import javabridge import bioformats matlFile = r'D:\barSeq\bxSeqIntTest_Cycle\matl.omp2info' img = bioformats.load_image(fileName) # Image data xmlRaw = bioformats.get_omexml_metadata(fileName) metadata = bioformats.OMEXML(xmlRaw) # OMEXML object w/ metadata print(metadata.image().get_Name()) # Should output 'bxSeqIntTest_A01_G001_0001.oir'
I’d like to get the XYZ physical coordinates for each plane in this file. I’m assuming this information is somewhere in the OMEXML object but I can’t seem to figure out exactly where. Has anyone managed to get this info out of an .oir file and could point out the method or property name to use?