Re: Fiji Bio-Formats is not opening large czi?

Posted by ctrueden on
URL: http://imagej.273.s1.nabble.com/Fiji-Bio-Formats-is-not-opening-large-czi-tp5011842p5011844.html

Hi Mario,

> Fiji shows "Analyzing XXX" in the status bar, then nothing happens.
> I've waited 20 minutes now, then gave up.

Did you try reading it with the Bio-Formats showinf command line tool?
http://openmicroscopy.org/info/bio-formats/users/comlinetools/

Did you check out the "Debugging JVM hangs" section of the Debugging page?
http://imagej.net/Debugging#Debugging_JVM_hangs

Getting a stack trace will tell you more about what is going on -- i.e.,
what Bio-Formats is doing internally, whether it has crashed, etc.

Did you try with the Bio-Formats update site enabled? This enables the
5.1.x development builds, which contain additional bug-fixes.
http://fiji.sc/Bio-Formats#Daily_builds

If this is a bug in Bio-Formats (if showinf also does not work, etc.), then
please report this bug to the OME team.
http://openmicroscopy.org/info/bio-formats/about/bug-reporting.html

Regards,
Curtis

On Tue, Mar 3, 2015 at 8:45 AM, Mario Emmenlauer <[hidden email]>
wrote:

> Hi,
>
> I have a 85 GB CZI file (one out of a series of 40 files in the
> same folder) that I wanted to open with latest Fiji (updates from
> today, on Win7 x64 with 42GB RAM, Sun Java 7, -Xmx 12GB. I tried:
>    Plugins > Bio-Formats > Bio-Formats Importer
>
> with options:
>  - View with Hyperstack
>  - Open files individually
>  - Use virtual stack
>  - all other options unchecked
>
> Fiji shows "Analyzing XXX" in the status bar, then nothing happens.
> I've waited 20 minutes now, then gave up. About Bio-Formats says
> "5.0.7 built 3.2.2015 revision 274796b".
>
> The file opens fine in Zeiss ZEN 2012 in ~30sec. I tried Fiji with
> the --debug option, but the command prompt console does not show any
> messages (to track down whats happening).
>
> Thanks for your help, and all the best,
>
>     Mario
>
>
>
>
> --
> Mario Emmenlauer BioDataAnalysis             Mobil: [phone]
> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
> D-81669 München                          http://www.biodataanalysis.de/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html