Posted by
Douglas Richardson on
URL: http://imagej.273.s1.nabble.com/Fiji-Bio-Formats-is-not-opening-large-czi-tp5011842p5011846.html
Hi Mario,
Is this a Lightsheet file that's been separated by time (or color, view,
etc.) so that you have a series of files in the format: filename.czi;
filename(1).czi; filename(2).czi? If so, open the complete file
(filename.czi) with Bioformats. You will then see a number of thumbnail
images representing filename(1).czi, filename(2).czi, etc. Check the one
you want to open. If you do not have enough RAM to open the file, make
sure you check "Open in virtual Stack."
This will take Fiji a long time to open (possibly minutes) as it has to
read all of the header data. Even longer than ZEN.
-Doug
On Tue, Mar 3, 2015 at 9:45 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
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http://www.biodataanalysis.de/>
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