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

[Zara Weinberg]

Thanks so much, David - that worked perfectly as a temporary workaround!

On Mon, Apr 23, 2018 at 11:52 AM Zara Weinberg <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> 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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