Matadata extraction from Nd2 files top at 12 lines in cellprofiler

#1

Hi I have encountered a strange problem when extracting the metadata for multi-series nikon nd2 files in cellprofiler. It seems that whenever the number of frames in each series is a factorial of 12 (3, 4 or 6 frames per series), only 12 lines/frames of metadata will be extracted. This does not happen when one series contains 5 frames for example where all the frames in the file can be read (>12 frames). I am wondering how to troubleshoot this problem? I am runing cellprofiler 3.19 in windows.

Thanks a lot!

Cheers,
Mingxi

#2

Hi @Mingxi, if you open the file directly with Bio-Formats do you see the same issue? Either via the command line tools (https://www.openmicroscopy.org/bio-formats/downloads/) or using the Bio-Formats Importer in FIJI is probably the easiest way to test. If you are seeing the issue with Bio-Formats on its own then it would be good if you could upload a sample file to https://www.openmicroscopy.org/qa2/qa/upload/ for testing.