Brightness gradient removal from images of microscope slides.

[Nicholas Verge]

Does anyone know of a plugin designed to remove brightness gradients
present across images of microscope slides

I ask, because I am new to ImageJ and have RGB 24bit images of rock thin-
sections which show such gradients. I would like to try as far as possible
to remove these gradients as they detract from the subject. Photoshop
plugins have proved to be of little use so I was hoping ImageJ users who
work with photomicrographs, may have developed something to do this job.

Any help or advice on this issue greatly appreciated.

Thanks,

Nicholas J. Verge BSc

[Joel Sheffield]

There are two options that you can try.
(1) Noel Bonnet (http://www.univ-reims.fr/Labos/INSERM514/ImageJ/)
has written a plugin called "A_posteri_Shading_Correction" .

(2) There is a standalone program available through the microscopy
web site (http://micro.magnet.fsu.edu) called "Background
subtraction".

Both of these allow you to place markers on the image that indicate
areas of common brightness, and then produce balanced images. There
are some limitations, though. Bonnet's works only on 8-bit images,
and the microscopy site program requires jpg files. Moreover, the
subtraction for RGB images can sometimes lead to odd color casts.

Good luck

Joel



Date sent: Thu, 28 Oct 2004 12:33:33 +0100
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Subject: Brightness gradient removal from images of microscope slides.

Post by Nicholas Verge
Does anyone know of a plugin designed to remove brightness gradients
present across images of microscope slides
I ask, because I am new to ImageJ and have RGB 24bit images of rock
thin- sections which show such gradients. I would like to try as far
as possible to remove these gradients as they detract from the
subject. Photoshop plugins have proved to be of little use so I was
hoping ImageJ users who work with photomicrographs, may have developed
something to do this job.
Any help or advice on this issue greatly appreciated.
Thanks,
Nicholas J. Verge BSc

Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: ***@temple.edu

[Nicholas Verge]

Post by Nicholas Verge
Does anyone know of a plugin designed to remove brightness gradients
present across images of microscope slides

Have you tried the Process>Subtract Background command?
-wayne

No I cant say I have, I will give it a try. I am still feeling my around
imageJ at the moment.

My problem is that for some of my slides there is not really a background
that can be subtracted, this is particualry true with thinsections
photographed using crossed polars.

However, using photoshop (curves)and dodge tool, I have had some success
using a non-linear contrast stretch to lighten the dakest parts of the
images without affecting the brightest, this can be improved by excluding
the ligther portions. However many of the images appear to far gone, so the
best solution is likely to be image cropping to leave the best parts.

Thank you for your advice.

Nick