[ome-users] LOCI question

[Melissa Linkert]

Hi Joaquim,

> I'm opening lif format images by drag-droping to FIJI's toolbar (LOCI menu is automatically open). The file I want to get some images from is 27.5 GB.
> 
> When I use an old version of FIJI I get the attached image1 (I can select which images to open from a list of small images list), whereas when I used an up-to-date version I get image2 (I am asked to define the image series to open) .
> 
> Image1 alternative is far more useful for me, is it possible to get the same as in image1 by using an up-to-date version of FIJI?

Not really, unfortunately.  The series chooser in image2 is expected if
there are more than 200 series in the file; this is due to a Java bug
which effectively limits how many thumbnails we can put into a single window.
See:

http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=5107980

Slightly older versions of Bio-Formats did not correctly split up image
series in some Leica .lif files (especially large tile scans).  I would
suspect that your file falls into that category, in which case image1
occurs because the series count was incorrectly detected as being
smaller than 200.

Regards,
-Melissa

On Fri, Sep 20, 2013 at 05:56:51PM +0200, Soriano.Joaquim wrote:
> Hi everyone!
> 
> I'm opening lif format images by drag-droping to FIJI's toolbar (LOCI menu is automatically open). The file I want to get some images from is 27.5 GB.
> 
> When I use an old version of FIJI I get the attached image1 (I can select which images to open from a list of small images list), whereas when I used an up-to-date version I get image2 (I am asked to define the image series to open) .
> 
> Image1 alternative is far more useful for me, is it possible to get the same as in image1 by using an up-to-date version of FIJI?
> 
> Thank you very much in advance.
> 
>  
> 
>  
> 
> Joaquim Soriano Felipe.
> 
> Confocal Microscopy Unit
> 
> Spanish National Cancer Research Centre (CNIO)
> 
> Melchor Fernández Almagro,3, E-28029 Madrid, Spain 
> 
> Phone  + 34 917 328 000, exts.: 3161, 3162. jsoriano at cnio.es
> 
>  
> 
>  
> 
> 
> 
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