Shading correction

[Fabiano Perina]

Hello all,

I'm kind a new ImageJ (Fiji) user and I wonder if you can help me.

I am trying to do shading correction on tiled  images generated by a High Speed
Confocal microscope. So does anyone know a plugin or macro to do this job using my reference image taken at the same conditions used for the multi tile images?

Since now I thank for your attention and time!
Best regards, Perina.

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[G. Esteban Fernandez]

Use Image Calculator (bare ImageJ) or Calculator Plus (Fiji) and perform a
divide operation between each tile and your shading reference image.  This
won't work if you already stitched all of your tiles together, in which
case you'll have to generate a stitched reference image.

In Image Calculator generate a 32-bit result.  In Calculator Plus multiply
by a konstant that is near the average pixel intensity of the tile.

-Esteban
On Jun 26, 2013 1:03 PM, "Fabiano Perina" <[hidden email]> wrote:

> Hello all,
>
> I'm kind a new ImageJ (Fiji) user and I wonder if you can help me.
>
> I am trying to do shading correction on tiled  images generated by a High
> Speed
> Confocal microscope. So does anyone know a plugin or macro to do this job
> using my reference image taken at the same conditions used for the multi
> tile images?
>
> Since now I thank for your attention and time!
> Best regards, Perina.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[Rob van 't Hof-2]

Hi,
use the shading corrector plugin from
http://rsbweb.nih.gov/ij/plugins/shading-corrector.html
or use my variant which prevents weird effects of overflow of 8-bit
values, and performs the colour shading by converting the image to HSB
format and does the correction on the B (brightness) band and leaves the
hue and saturation as they are. for me that often works better.

You can get my variant at:
https://dl.dropboxusercontent.com/u/50702312/Shading_Corrector_RvH.class
https://dl.dropboxusercontent.com/u/50702312/Shading_Corrector_RvH.java

Both variant look for a reference image with the name "blank-field", so
rename your reference image like this.

Hope this helps,
Rob

On 26/06/2013 20:49, Fabiano Perina wrote:

> Hello all,
>
> I'm kind a new ImageJ (Fiji) user and I wonder if you can help me.
>
> I am trying to do shading correction on tiled  images generated by a High Speed
> Confocal microscope. So does anyone know a plugin or macro to do this job using my reference image taken at the same conditions used for the multi tile images?
>
> Since now I thank for your attention and time!
> Best regards, Perina.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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_____________________________
Dr. Rob van 't Hof
Reader

Centre for Molecular Medicine
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road, Edinburgh EH4 2XU
United Kingdom

Phone: [phone]
email: [hidden email]
_____________________________

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[Fabiano Perina]

Thank you very much for your help Rob, very helpful  I'll try it!

Best regards, Perina

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[Fabiano Perina]

Thank you so much for your help Esteban,  I'll try it!

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[pang]

Esteban and Fabiano,

In Image Calculator generate a 32-bit result.  In Calculator Plus multiply by a konstant that is near the average pixel intensity of the tile.
Why don't you multiple a constant that is the maximum of your reference image (smoothed). I think it is better than using the average.

Zhengyu

Zhengyu Pang, Ph.D.
Biochemistry and Bioanalytics Laboratory
Diagnostic and Biomedical Technologies
GE Global Research, K1-5B37A
One Research Circle
Niskayuna, NY 12309
T: 518-387-4015
F: 518-387-7765



-Esteban
On Jun 26, 2013 1:03 PM, "Fabiano Perina" <[hidden email]> wrote:

> Hello all,
>
> I'm kind a new ImageJ (Fiji) user and I wonder if you can help me.
>
> I am trying to do shading correction on tiled  images generated by a
> High Speed Confocal microscope. So does anyone know a plugin or macro
> to do this job using my reference image taken at the same conditions
> used for the multi tile images?
>
> Since now I thank for your attention and time!
> Best regards, Perina.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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[G. Esteban Fernandez]

You're right, I use average for transmitted light images (brightfield) and
max for fluorescence images. Thanks for the correction.

-Esteban
On Jun 27, 2013 6:55 AM, "Pang, Zhengyu (GE Global Research)" <[hidden email]>
wrote:

> Esteban and Fabiano,
>
> In Image Calculator generate a 32-bit result.  In Calculator Plus multiply
> by a konstant that is near the average pixel intensity of the tile.
> Why don't you multiple a constant that is the maximum of your reference
> image (smoothed). I think it is better than using the average.
>
> Zhengyu
>
> Zhengyu Pang, Ph.D.
> Biochemistry and Bioanalytics Laboratory
> Diagnostic and Biomedical Technologies
> GE Global Research, K1-5B37A
> One Research Circle
> Niskayuna, NY 12309
> T: 518-387-4015
> F: 518-387-7765
>
>
>
> -Esteban
> On Jun 26, 2013 1:03 PM, "Fabiano Perina" <[hidden email]> wrote:
>
> > Hello all,
> >
> > I'm kind a new ImageJ (Fiji) user and I wonder if you can help me.
> >
> > I am trying to do shading correction on tiled  images generated by a
> > High Speed Confocal microscope. So does anyone know a plugin or macro
> > to do this job using my reference image taken at the same conditions
> > used for the multi tile images?
> >
> > Since now I thank for your attention and time!
> > Best regards, Perina.
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

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