I have a set of images from Aperio (
svs) and Roche (
bif) I would like to get all the metadata available.
Concretely I am mostly interested in the biopsy information that these WSI would bear. I am actually trying to deidentify them and I would check every possible field to be sure all the information has been removed.
For now, I am able to got the scanner information by doing something like:
import javabridge import bioformats import bioformats.formatreader as F from bioformats import metadatatools javabridge.start_vm(class_path=bioformats.JARS) file = "LEICA/SVS/image1.svs" ImageReader = F.make_image_reader_class() reader = ImageReader() omeMeta = bioformats.metadatatools.createOMEXMLMetadata() reader.setMetadataStore(omeMeta) reader.allowOpenToCheckType(True) reader.setId(file)
If here I do
reader.getMetadata(), it only prints something like
<Java object at 0x4f656148>