Posted by
Mario Emmenlauer-3 on
URL: http://imagej.273.s1.nabble.com/Fiji-Bio-Formats-is-not-opening-large-czi-tp5011842p5011874.html
Hi Curtis,
On 03.03.2015 17:11, Curtis Rueden wrote:
>> 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/I tried that now, and it seems Stephan Preibisch might be right that
opening the files just takes forever. But why? The network mount is
reasonably fast, it achieves easily 100MB/s. Zeiss Zen 2012 opens the
file in ~30sec, and I can scroll through the timepoints and stacks at
reasonable speed. I opened the czi with "Open files individually" and
"Use virtual stack" in Fiji, and I hoped this might speed things up.
So in Fiji, I can select the thumbnails finally after > 2hrs. Thats
25% of the time it would take to read *all* the files over the 100MB/s
network. I can not think Bio-Formats would not read 25% of the 4TB
data, just to show thumbnails?
When using showinf, it prints first:
Checking file format [Zeiss CZI]
Initializing reader
ZeissCZIReader initializing L:\MarioEmmenlauer\Lightsheet_RAW\drlGFP lmo2Red 7ss .czi
... and then after around 1 hour, it fails with out-of-memory. Can
it really take >2 hrs before I can see anything? Should the option
"Open files individually" not limit it to the first timepoint?
Cheers,
Mario
> 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: +49-(0)151-68108489
>> 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>
--
A: Yes.
> Q: Are you sure?
>> A: Because it reverses the logical flow of conversation.
>>> Q: Why is top posting annoying in email?
Mario Emmenlauer BioDataAnalysis Mobil: +49-(0)151-68108489
Balanstrasse 43 mailto: mario.emmenlauer * unibas.ch
D-81669 München
http://www.biodataanalysis.de/--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html