http://imagej.273.s1.nabble.com/Fiji-Bio-Formats-is-not-opening-large-czi-tp5011842p5011877.html
> forever. But why? The network mount is reasonably fast, it achieves
while you are waiting for the files to be read. Just press Ctrl+\ while
showinf is thinking. Cut and paste them from your console, saving them to
files. Look for the string "loci.formats." and find out which Bio-Formats
classes/method/lines are being hit. That will be 90% likely to answer your
> 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>