Open Microscopy Environment

I have a group of normal (uncropped, unmodified) .nd2 files that were collected on the same day and have the same basic structure (number of fields, number of z-slices, number of channels; only difference is the number of time points). `showinf` returns incorrect metadata for one of the files (the largest, ~100 GB). Specifically, the file has 18 series, 16 time points, and 31 z-slices per time point. There should be 16*31=496 planes per series, but `showinf` reports 499 planes, sizeT=1, sizeZ=499. All the other files are processed correctly (e.g., sizeT=4, sizeZ=31). Since all but one file is processed correctly by `showinf` and the files are ostensibly similar, the reason for the anomalous behavior on one of the input files is unclear.

Since the file is probably too large to upload to OME, is there a way to extract the metadata of the .nd2 file in binary form (e.g., using known or computable offsets)? If so, I could provide the binary metadata from two .nd2 files, one of which is interpreted correctly by `showinf` and one of which is interpreted incorrectly. Thanks.

Thank you for reporting this problem.

There is not currently a way to report the metadata that would be relevant for debugging this problem without sending the .nd2 file itself. We will consider adding a way to do this in the next release of Bio-Formats (see https://trello.com/c/Y4KMCatE/19-nd2-ch ... speedup-pr).

However, if you are willing to send the file, that will still be the fastest and easiest way to fix the problem. While 100GB is too large for QA, we do have an FTP server that can be used for such large files; credentials are being sent in a private message.