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

Posted by Mario Emmenlauer-3 on
URL: http://imagej.273.s1.nabble.com/Fiji-Bio-Formats-is-not-opening-large-czi-tp5011842p5011864.html

Hi,

On 03.03.2015 18:45, Stephan Preibisch wrote:
> I did not experience this problem using Bioformats so far, even for very long timelapses acquired with the Lightsheet Z.1.
>
> You can try my Multiview Reconstruction pipeline which is part of Fiji (http://fiji.sc/Multiview-Reconstruction <http://fiji.sc/Multiview-Reconstruction>) to test it. Just
>
> 1) Define a new XML dataset (Plugins > Multiview Reconstruction > Define Multi-View Dataset). Press OK, then choose the first filename.CZI (the one without (1), (2), etc.)
> 2) It will show all the metadata and you should just have to click OK.
> 3) Then, for example display one of the views (Plugins > Multiview Reconstruction > Tools > Display View)

I tried this, also this seems not to work. Here is what I see:

 1) Define a new XML dataset (Plugins > Multiview Reconstruction > Define Multi-View Dataset). Press OK, then choose drlGFPlmo2Red7ss.czi
 2) It shows in the log window:

    2
    Investigating file 'L:\MarioEmmenlauer\Lightsheet_RAW\drlGFPlmo2Red7ss.czi'.

No output comes after that in a very long time.

All the best,

    Mario

> You can also resave the entire or parts of the dataset as TIFF or HDF5 (Plugins > Multiview Reconstruction > Resave > As TIFF). It also supports registration, fusion, deconvolution of the dataset!
>
> Hope this helps,
> Stephan
> ---
>
> Dr. Stephan Preibisch
> HFSP Fellow
> Robert H. Singer / Eugene Myers lab
>
> Albert Einstein College of Medicine / HHMI Janelia Farm / MPI-CBG
>
> email: [hidden email] <mailto:[hidden email]> / [hidden email] <mailto:[hidden email]> / [hidden email] <mailto:[hidden email]>
> web: http://www.preibisch.net/ <http://fly.mpi-cbg.de/preibisch>
>> On Mar 3, 2015, at 11:49 , Douglas Richardson <[hidden email]> wrote:
>>
>> 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: [phone]
>>> Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
>>> D-81669 München                          http://www.biodataanalysis.de/
>>>
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>>>
>>
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>
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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: [phone]
Balanstrasse 43                    mailto: mario.emmenlauer * unibas.ch
D-81669 München                          http://www.biodataanalysis.de/

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