I have plate data from Nikon confocal microscope in nd2 file format that I would like to import in OMERO. Using both fiji or OMERO gives incorrect series. Each serie contains image planes from different positions instead of real time planes.
ND2 file contains multiple positions with following dimensions:
|Series 0 Name|Seq0000.nd2 (series 01)|
While ND2 dimonsionorder is: Dimensions T(61) x XY(12) x Z (1)
XY(12) reflects to 12 positions in the test dataset
I assume it is indexing problem of how bioformats interprets series (or Nis-element is not following any standards). I tried bioformats import options with changing stack order (view stack with: standard imagej) without any success.
Other plate data files from the same microscope gives same issue, while not plate data files don’t have this issue. Apparently, nd2 plate files have different indexing then regular nd2 files.
Is there a way to correctly import/read this data in OMERO?
Any help or suggestions will be appreciated.