Bioformats reads .nd2 file series incorrectly


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)|
| SizeC|2|
| SizeT|61|
| SizeX|512|
| SizeY|512|
| SizeZ|1|

Bioformats reads:
DimensionOrder XYCZT

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.


1 Like

I wonder if this is Nd2: support for SPW datasets rearing its head. Would you be able to make sample data available to us, perhaps via Ideal is if it is public data but just let us know if you need the plate kept confidential.

Hello Mark,

Dataset is not mine, but I don’t think anybody can make any sense of the data anyway. I asked permission from owner, but keeping it confidential meanwhile will be great until I get response.

File is now uploaded: seq0000.nd2 It is the smallest file size I could get for testing. I am trying to help users with importing datasets in OMERO.

I can get the order right using fiji, merging all series in a single stack and then creating a hyperstack. Since z is only 1, I can use z-dimension for series. But I do need to merge all series to get all planes first, and this method will not work for usual multi-z acquisition datasets.

Hope you can make more sense out of it.

Best, Rohola

Thanks for uploading the sample file @rohola. I was able to reproduce the bug with Bio-Formats 6.3.1 as you described. I have opened a GitHub Issue to track the bug: