[SCIFIO] Bio-Formats + ITK loading image so slow

[Curtis Rueden]

Hi Yu,

> In that case, there is already an entry in the issue tracker for this
> problem:
>
>   https://github.com/scifio/scifio-imageio/issues/17

Actually, it looks like the issue above is regarding memory performance.
You might want to file a new issue regarding time performance, if your
research confirms that the culprit is the SCIFIO ImageIO component.

Thanks,
Curtis

On Thu, Dec 18, 2014 at 2:29 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>
> Hi Yu,
>
> > But the problem is, the image loading time is so long! It takes almost
> > 10 minutes to load a 2 Gigs svs image! Is this normal?
>
> I would suggest trying to load your image in Fiji via the Bio-Formats
> Importer plugin:
>
>   http://fiji.sc/Bio-Formats
>
> And see whether the load time is equivalent, or much faster.
>
> If the load time is similar, then it is a limitation of Bio-Formats. In
> that case, you can file an issue with the Bio-Formats team:
>
>   http://openmicroscopy.org/info/bio-formats/about/bug-reporting.html
>
> If the load time is much faster, then the problem is with the SCIFIO
> ImageIO plugin. In that case, there is already an entry in the issue
> tracker for this problem:
>
>   https://github.com/scifio/scifio-imageio/issues/17
>
> Feel free to comment on the issue if you want to be notified of progress.
>
> Regards,
> Curtis
>
> On Mon, Dec 8, 2014 at 9:59 AM, Yu Zhou <yxz949 at case.edu> wrote:
>
>> Hi folks,
>>
>>
>> I am developing a pathology image analysis tool using ITK and Qt. In my program, I tried to use Bio-Formats to load big svs/TIFF images. I have successfully used itkSCIFIO and loaded a 20M image and did some image processing. But when I tried to load big images larger than 2 Gigs, I have to use streaming to avoid memory allocation error. But the problem is, the image loading time is so long! It takes almost 10 minutes to load a 2 Gigs svs image! Is this normal? Does anyone known how to solve this problem? Could you please give me some suggestion on it? Thank you so much!
>>
>>
>> Yu
>>
>>
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