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

[David Gault (Staff)]

Hi Zara,

Placing the jar in the jars/bio-formats folder as you have done should be enough to update the version, however it seems that it is still missing a dependency. Using the complete library https://mvnrepository.com/artifact/edu.ucar/netcdfAll/4.6.11 which includes all the optional components and dependencies is probably the easiest solution in this instance. I have updated the Trello card (https://trello.com/c/VrpWk1Fj/119-netcdf-update) to further investigate which specific component or dependency was the cause of the issue seen here.

With Thanks,
David Gault

On 23 Apr 2018, at 16:52, Zara Weinberg <weinberz at umich.edu<mailto:weinberz at umich.edu>> wrote:

Thanks so much for the fast reply, David. While waiting for the Trello issue to resolve, is it possible for me to use your workaround on my local system? I attempted to download the same version of netcdf you mentioned from https://mvnrepository.com/artifact/edu.ucar/netcdf4/4.6.11, and copied it into my Fiji.app/jars/bio-formats/ folder, but I am still getting the same error upon opening the file. Any suggestion?

On Sat, Apr 21, 2018 at 4:13 PM 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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