[ome-users] Bio-Formats not opening Imaris file with several thousand slices

[David Gault (Staff)]

Hi Zara,

Thank you for submitting the QA files. I was able to test and reproduce the problems you were seeing with the latest Bio-Formats release.

This issue appears to be caused by the fact that Bio-Formats currently uses an older version of the NetCDF library. I have tested the files in FIJI with a more recent version of the NetCDF jar and this allows the files to be opened and read. We have an ongoing investigation into upgrading the NetCDF dependency and I have updated the existing Trello card with details from your submitted QA.

https://trello.com/c/VrpWk1Fj/119-netcdf-update

With Thanks,
David Gault


On 21 Apr 2018, at 21:13, Zara Weinberg <weinberz at umich.edu<mailto:weinberz at umich.edu>> wrote:

Hello,

I'm acquiring high speed microscopy movies with many frames (~50hz, 6000 frames per movie). My microscope software automatically saves these files as .ims files, compatible with Imaris 9.0 (I'm guessing these are Imaris 5.5 files, given that). Bio-Formats has no trouble opening much smaller files from the software, but when trying to open these files in Fiji, I get the following error:

"[ERROR] bad version 72 at filePos 674029
[ERROR] bad version -29 at filePos 677106
[ERROR] bad version 0 at filePos 677155
[ERROR] bad version 66 at filePos 677103
[ERROR] bad version 20 at filePos 677128
[ERROR] bad version 0 at filePos 677146"

With a dialog box that pops up saying the file is incompatible. Notably, these files open trivially in Imaris.

Version Information: Mac OS X 10.12.6, ImageJ 1.51w, Bio-Formats 5.8.1, Java 1.8.0_66 (64-bit)
An example file (with Metadata) has been uploaded at https://www.openmicroscopy.org/qa2/qa/feedback/20628/. 2018-04-19_18.26.38_Sample Prefix_2V7DQK2_Protocol.ims is a file that doesn't import, but 2018-04-16_18.58.13_Sample Prefix_2V7DQK2_Protocol_F01.ims is a file that imports just fine from the same software (albeit having many fewer frames).

Thanks so much for any help you can give!
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