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-tp5011842p5011851.html

Hi Mario,

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)

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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