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

[Curtis Rueden]

Hi Gaëtan,

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

Great. And we will eliminate the problem for TIFF files soon as well.

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.
>

That is bad news. I was planning on doing some benchmarks comparing with
Bio-Formats + Ice, but was not expecting to see such bad performance with
JNI. I will look into it and see what I can find out. It should be possible
to do much better.

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


Thank you.

-Curtis

2009/5/20 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>

>
> 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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