Fiji: New Filter "Normalize Local Contrast"

[Stephan Saalfeld]

Hi,

I added a new filter to Fiji:

Plugins->Integral Image Filters->Normalize Local Contrast

It adjusts local contrast resulting in an effect that superficially
reminds to CLAHE.  It is however solely based on block-statistics: mean
and STD, no histograms involved.  The nice point compared with CLAHE is
that each pixel is processed truly individually and still it is as fast
thanks to using integral images for calculating the block-statistics.

Do not forget to check the preview checkbox for testing.

I use the filter to correct for uneven illumination and to compensate
for artifacts that introduce a large contrast shift in 16bit images.  I
hope it's useful for somebody.

Best,
Stephan

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[godblessfq]

Hi Stephan,
This plugin doesn't work on a stack. It says it will do the normalization on all images, but nothing happens.
Can you fix it?
Thank you very much!
Eric

[Stephan Saalfeld]

Hi Eric,

sure?  For me it does.  Can you try starting Fiji from a terminal and
see if it prints something evil?  There were numerous changes in the
updating system and other parts of the Fiji infrastructure during the
last few months that sometimes left Fiji in an inconsistent state.  If
it doesn't work after Help>Update Fiji, then please tell me again.

Best,
Stephan




On Sat, 2013-01-12 at 19:58 -0800, godblessfq wrote:

> Hi Stephan,
> This plugin doesn't work on a stack. It says it will do the normalization on
> all images, but nothing happens.
> Can you fix it?
> Thank you very much!
> Eric
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/Fiji-New-Filter-Normalize-Local-Contrast-tp4999077p5001387.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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[godblessfq]

Thank you Stephan. Now I am sure it's the problem with my installation and I have circumvented it using a simple macro.
Hope this is helpful to anyone who has the same problem. Here is the macro:
a=nSlices;
for (i=1; i<a; i++)
{    setSlice(i)
    run("Normalize Local Contrast", "block_radius_x=8 block_radius_y=8 standard_deviations=3 center stretch slice");
}

On 14/01/2013 2:54 PM, Stephan Saalfeld [via ImageJ] wrote:

Hi Eric,

sure?  For me it does.  Can you try starting Fiji from a terminal and
see if it prints something evil?  There were numerous changes in the
updating system and other parts of the Fiji infrastructure during the
last few months that sometimes left Fiji in an inconsistent state.  If
it doesn't work after Help>Update Fiji, then please tell me again.

Best,
Stephan




On Sat, 2013-01-12 at 19:58 -0800, godblessfq wrote:

> Hi Stephan,
> This plugin doesn't work on a stack. It says it will do the normalization on
> all images, but nothing happens.
> Can you fix it?
> Thank you very much!
> Eric
>
>
>
> --
> View this message in context: http://imagej.1557.n6.nabble.com/Fiji-New-Filter-Normalize-Local-Contrast-tp4999077p5001387.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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