.ND2 metadata and import issues

Usage & Issues
#1

Hi all,

Nikon .nd2 files created with recent versions of NIS elements seem to have a few issues when using bio-formats for import.
This seems to be due to the metadata.

  1. Timestamps are no longer correctly imported. Whilst there are values in the metadata file, they do not make sense.
    2.Series (created when performing multi-point acquisitions) are now being imported as z-stacks.
    I am not sure whether the responsibility for this lies with Nikon or you guys but wanted to flag this as an issue that impairs existing workflows.

Cheers,
James

#2

Hi James, thanks for rasining the issues. We have seen quite a few reports of issues withr ecent NIS versions. The first timestamp issue looks similar to https://github.com/ome/bioformats/issues/3565

If you have a sample file that we could use for testing you can upload it to https://www.openmicroscopy.org/qa2/qa/upload/ along with the correct expected values.

The second issue may be related to https://github.com/ome/bioformats/issues/3502 but I would need to test a sample file to confirm. Again if you have a test file which could uploaded that would be a great help.

#3

Hello guys,

please look into this one, it seems to be a more than a year old issue - from version 5.10 or 5.11 of NIS-Elements. I would really appreciate it, since I make quite a few videos on daily bases and to get time stamps I have to open and save the acquired data in the older versions of NIS making double copies of everything.

I can upload more data if necessary (I already uploaded some in January 2020).

Thanks a lot for your help!
Cheers,
Jan

#4

Hi Jan, thanks for the offer, any additional sample files you have would be a great help for our testing.

#5

Hi david,

i can also provide some sample data that is imported incorrectly if needed, please let me know

#6

Hi @Joost_Willemse1, any additional sample files showing issues are always welcome and can be uploaded to https://www.openmicroscopy.org/qa2/qa/upload/. If the files are larger than 2GB then you can send me a private message here with an email address I can use to arrange for ftp access to transfer files instead.