[Insight-users] Bio-Formats in ITK (was: Re: ITK for fluorescence microscopy - BioImageXD)

[Gaëtan Lehmann]

Le 20 mai 09 à 14:58, Curtis Rueden a écrit :

> Hi Gaëtan,
>
> -      "jace-runtime.jar:bio-formats.jar:loci_tools.jar"
> +      "jace.jar:jace-runtime.jar:bio-formats.jar:loci_tools.jar"
>
> Interesting; this library is not supposed to be necessary. But I'm  
> glad you got it working.
>
> Any idea about what is wrong with the threads?
> Also, do you now why it tries to start AWT? A GUI shouldn't be  
> useful in that case!
>
> We are aware of the AWT error messages on Mac OS X, and are working  
> to fix them. It is basically a matter of removing references to the  
> java.awt.Rectangle class, which we use for convenience reasons right  
> now, but can easily be changed.
>
> In the meantime, would you mind trying to read a file in a non-TIFF- 
> based format? The AWT errors mainly happen with TIFF-based formats  
> with the current codebase.
>

I don't get that error with a zvi file. Great!

However, the performances don't seem that good: with my simple python  
wrapper for bioformats, I open the image in 39 seconds.
With itk-plugin, at 39 second, only 6 plans are open on the 51 plans  
of the image.

I'll continue my investigations and will continue to report my progress.

Regards,

Gaëtan


-- 
Gaëtan Lehmann
Biologie du Développement et de la Reproduction
INRA de Jouy-en-Josas (France)
tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
http://voxel.jouy.inra.fr  http://www.mandriva.org
http://www.itk.org  http://www.clavier-dvorak.org

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