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

Posted by Stephan Preibisch on
URL: http://imagej.273.s1.nabble.com/Fiji-Bio-Formats-is-not-opening-large-czi-tp5011842p5011865.html

Yes, this might be the issue … over the network it might be much slower from my experience.

Cheers,
Stephan

> On Mar 4, 2015, at 7:28 , Mario Emmenlauer <[hidden email]> wrote:
>
> 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] <mailto:[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
>>
>
> --
> 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: [phone]
> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch <http://unibas.ch/>
> D-81669 München                          http://www.biodataanalysis.de/ <http://www.biodataanalysis.de/>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html <http://imagej.nih.gov/ij/list.html>

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