Posted by
Mario Emmenlauer-3 on
URL: http://imagej.273.s1.nabble.com/Fiji-Bio-Formats-is-not-opening-large-czi-tp5011842p5011863.html
Hi,
On 03.03.2015 17:49, Douglas Richardson wrote:
> 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."
Yes, its a Lightsheet file that has been separated by time. I tried
to open the complete file drlGFPlmo2Red7ss.czi with Bio-Formats, and
nothing shows up, even after many minutes (no thumnails, no popup,
no status message, nothing). Its as if I never tried "open" at all.
Fiji just stands there, idle...
Could it be that opening files from a (very fast fiber-connected)
network share (mounted as drive letter L:) is not supported?
All the best,
Mario
> 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
>> D-81669 München
http://www.biodataanalysis.de/>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
> --
> ImageJ mailing list:
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--
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