Dear All,
We recently received a data submission on our QA system and several private emails requesting help for the Nikon .nex file format. We indicated in our responses that we much prefer to run discussions about file formats or other issues on these open lists. This allows everyone in the community to benefit from and contribute to the discussion about the format. We thought it would be useful to share the discussion publicly, in case anyone was interested.
As always, we will keep this data confidential, just as we do for the rest of the >600,000 files submitted to our data repository. We only make data publicly available (e.g., at http://downloads.openmicroscopy.org/images/) if a submitting author has explicitly granted us permission to do so.
Regarding opening the submitted files, we are able to open the individual .ics files in Fiji with the latest version of Bio-Formats (5.1.8). This might be a partial solution to accessing these files.
Regarding support for Nikon .nex files, they are currently not one of our supported formats [1]. As the submitter correctly noted, we have an open ticket to add support for this format [2]. It has been open for several years, but this submission is the first example of this file format we’ve received. As stated previously [3], we can’t initiate work on a file format until we have real data to work with, and to use for testing. If anyone else in the community has good examples of this format, we’d very much appreciate receiving more samples to work with.
As explained in a recent blog post [4], most of our Bio-Formats efforts for the upcoming 5.2.0 version are focused on improvements to our handling of Regions of Interest (ROIs). For this reason, we have decided not to add support for any new file formats, so this is why the ticket linked above is still marked as Unscheduled. If anyone would like to be cc’d on this ticket, let us know, so you’ll be notified as soon as the status changes.
Thanks again for the .nex data submission.
Cheers,
Jason
[1] https://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html
[2] https://trac.openmicroscopy.org/ome/ticket/4113
[3] http://blog.openmicroscopy.org/file-formats/community/2014/11/14/partnership/
[4] http://blog.openmicroscopy.org/file-formats/data-model/future-plans/2016/01/26/bf-model-status/
