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

Zara Weinberg weinberz at umich.edu
Mon Apr 23 16:52:42 BST 2018


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> 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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