Hi Aaron,
OME Bioformats support for the Olympus raw file format (.oir) is incomplete. When a .oir file reaches a size larger than 1Gb, Olympus automatically begins splitting the file into sub-files, e.g. 'datafile.oir' will contain time points 0 through N, then 'datafile_00001' will contain time points N through M, etc... These files need to be loaded/treated as one large file, but OME Bioformats does not do this properly. (Note: the sub-files cannot simply be loaded as separate .oir files. See my previous post).
Linking back to
viewtopic.php?f=13&t=8360 for the previous post mentioned above. From the OME standpoint, a short summary is that the Olympus OIR reader has no support for OIR datasets composed of multiple files such as the ones discussed above and in the previous thread. This is primarily due to the fact we had no such representative samples when the initial OIRReader was developed for Bio-Formats 5.5.0.
I would greatly appreciate Bioformats correcting this issue. If I upload a complete example of a large split .oir file, could someone work on this?
From the OME side, we can certainly record this format support addition in our public backlog. Given our current agenda and deadlines, it is unlikely the open-source team will have the time to prioritize this issue in the upcoming months.
It is possible that someone in the growing Bio-Formats contributing community can and wants to get involved. For this to happen, sharing representative datasets publicly is probably the best starting point if possible (see
http://downloads.openmicroscopy.org/images/Olympus-OIR/ for instance).
Note, the Olympus Viewer ImageJ plugin handles these split files correctly, but it is not scriptable or usable outside of ImageJ.
Knowing that the Olympus Viewer ImageJ plugin works on this file is certainly great to hear since this is the
reference external software we used to validate OIR filesets during the initial reader development.
Best,
Sebastien
