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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[Rob van 't Hof]

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

Post by 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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_____________________________
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: rob.vanthof-***@public.gmane.org
_____________________________

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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

Post by 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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Pang, Zhengyu (GE Global Research)]

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

Post by 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.
--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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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

Post by Pang, Zhengyu (GE Global Research)
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

Post by 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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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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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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