Is there an option to extract the metadata from the file header complete/unaltered directly into a text file? I know there are a few pieces of metadata information that are not input into the cellprofiler metadata module, but are important for downstream analysis. I am using a nd2 filetype.
To my knowledge, no; given that every manufacturer’s container format is both structured differently and contains different information, it’s not really within the scope of CP to try to parse them all, other than looking for the few key pieces of metadata that are common to most analyses. I image Nikon Elements or OMERO could do the job though, and if you wanted to incorporate those metadata into a CP pipeline the Metadata module can read CSVs.