Nikon ND2 file import issue

HI,

We just installed a Nikon system that uses NIS Elements and is meant to be used for high content screening. One initial acquisition of a screen resulted in a directory of nd2 files for each well (still figuring out how to make Elements treat the whole plate as a single experiment). Anyway, we acquired 4 fields per well and in OMERO only the first field shows up (omero 5.0.2), using the command line importer. I'm uploading the file for Well A1 to the QA system (#9438).
Fiji's BioFormats importer (5.0.2-DEV - 29 July 2014) interprets the file as having 4 time points. Also not correct but better than ignoring the 3 fields. Will 5.0.3 have better handling of multi-location ND2's?Second problem: for the "Pixels Size (XYZ) (µm)" only the X value is interpreted correctly and it shows 0.0 for Y. Maybe the Y value was missing from the file?? Would it be acceptable kludge for the importer to assume the same pixel size value for Y as for X if that value is not in the ND2 file?

please help

I did not find the right solution from the internet.

References:
https://www.openmicroscopy.org/community/viewtopic.php?f=13&t=7588
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Thanks

Comments

  • spraynprayspraynpray Posts: 5,982Moderator
    Hi kevinmanuel, Welcome to NR.

    I fear your enquiry is a little specialised for this forum, and judging by the openmicroscopy thread you linked to above, it looks like you have already done the best thing which is to contact the system supplier.

    Good luck in finding a solution though.
    Always learning.
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