Incomplete import of Nikon nd2 files

bio-formats
Tags: #<Tag:0x00007fd542b83138>

#1

I am trying to load a relatively large (5.8 GB) Nikon .nd2 file with three channels and 232 frames. Fiji (via the bio-formats importer) can open the file, but loads/displays only the first 86 frames, rather than the whole time series. My first thought was that this was a memory issue, but that doesn’t seem to be the case; the data that it loads takes only 2 GB, and I have 12 GB of memory available. Also, using virtual stack doesn’t alter the behavior. Perhaps a bug in bio-formats?

The particulars:
IJ version 2.0.0-rc-65/1.51s, updated today (2/8/18).
Bio-formats version 5.7.3 (1/11/18)
Running on Mac OSX 10.12.6

Thanks for any suggestions.


#2

Have a look at this old thread for a possible solution: