normalize part of image according to another part

[Vojtas]

Dear all,

I have a scanned 16 bit grayscale image that has an artifact - part of the image has lower dynamic range of pixel intensity. I would like to adjust the range of pixel intensity according to a selected part of the image and preserve the "healthy" part of the image.

I am not satisfied with histogram normalization/equalization. I kind of like a plugin Quantile Based Normalization (Fiji), -  http://www.longair.net/edinburgh/imagej/quantile-normalization/ 
but I couldn't make it work the way I wanted. I was not able to apply successfully the mask for the selected part of image. Also, when I tried the plugin on two testing images, I ended up with two processed images both with changed pixel intensity. I wonder if there is a way how to mark one image as "source" of pixel intensity histogram.

Any suggestions how to either make the Quantile Based Normalization work or to adjust the histogram of one part image according to another?

Vojta

"healthy" image part:

[gankaku]

Hi Vojta,

You might want to try a pseudo flat-field correction (
http://fiji.sc/BioVoxxel_Toolbox#Flat-field_and_Pseudo_flat-field_correction
).
If you are not using Fiji but ImageJ you can separately download the
toolbox from

http://www.biovoxxel.de/BioVoxxel%20Macro%20Toolset/BioVoxxel_Toolbox.ijm

and save it in the macros\toolset folder and select it from the >> icon.

this might not work perfectly at the transition between the bright and the
dark region but will make the different intensities more equal.

regards,
Jan



2014-04-24 12:50 GMT+02:00 Vojtas <[hidden email]>:

> Dear all,
>
> I have a scanned 16 bit grayscale image that has an artifact - part of the
> image has lower dynamic range of pixel intensity. I would like to adjust
> the
> range of pixel intensity according to a selected part of the image and
> preserve the "healthy" part of the image.
>
> I am not satisfied with histogram normalization/equalization. I kind of
> like
> a plugin Quantile Based Normalization (Fiji), -
> http://www.longair.net/edinburgh/imagej/quantile-normalization/
> but I couldn't make it work the way I wanted. I was not able to apply
> successfully the mask for the selected part of image. Also, when I tried
> the
> plugin on two testing images, I ended up with two processed images both
> with
> changed pixel intensity. I wonder if there is a way how to mark one image
> as
> "source" of pixel intensity histogram.
>
> Any suggestions how to either make the Quantile Based Normalization work or
> to adjust the histogram of one part image according to another?
>
> Vojta
>
> "healthy" image part:
> <http://imagej.1557.x6.nabble.com/file/n5007413/area.gif>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/normalize-part-of-image-according-to-another-part-tp5007413.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Vojtas]

Hello Jan,

thank you for your advice. I am not sure if I am using the pseudo flat-field correction right, but after selecting the area to be corrected, there is just bluring of the area as I tune up the sigma parameter. I hoped that the intensity values in the artefact area could be rescaled according to the rest of the image.

Best,

Vojta