Re: Optical artefact removal

Posted by John J. Bozzola on Jul 18, 2006; 7:16pm
URL: http://imagej.273.s1.nabble.com/Optical-artefact-removal-tp3702076p3702080.html

We have this "affliction" all the time since we are using a digital
camera on a transmission electron microscope and the phosphor (not
being smoothly applied) has a bright quadrant. NIH does an excellent
job of subracting the background. Basically, you record an image
under the same lighting conditions as the specimen (but minus the
specimen). This gives the background that you want to subtract. Next
record your image under the same lighting conditions (relative
brightness). Open both images, go to Process/Math and subtract the
background from the image. It does a super job. Now, I must admit
that I am not using Image J but I am sure these features are there as
well.

John

>
>I have had an enquiry from someone from another Department who has an
>artefact affecting their imaging which looks like a diffraction effect
>(e.g. Newton rings) when doing transmitted light microscopy.
>
>
>
>I had a look at their microscope and camera system and even when Koehler
>illumination is set up properly, you still get this effect. The
>microscope is a rather old Nikon inverted microscope with a Coolpix
>attached. The objectives, (phase contrast), are not infinity corrected
>and I'm assuming that there is also a problem with the tube length for
>the camera. The rings are there irrespective whether specimens are on
>glass or in plastic dishes. I don't think much can be done optically
>(correct me if I'm wrong) but I wondered if some image processing could
>help.
>
>
>
>My ImageJ question is this:
>
>
>
>Is it possible to use some kind of image processing (e.g. image
>subtraction) to remove this artifact? I have tried a few things out
>(e.g. Image calculator, rolling ball) without much success so far.
>
>
>
>I have posted 2 images at the following address:
>http://www.health.auckland.ac.nz/biru/exptal_images/index.html There are
>also links to larger images although the original images are even larger
>than these.
>
>
>
>Please note that I do know that these images are appalling! I asked one
>of the students to send me one image with tissue (glass slide) and one
>without at the same focal plane and this is what I got! I don't think
>they set up the microscope very well. However, you can see the rings
>clearly on both images so I hope they will inspire someone to suggest a
>solution.
>
>
>
>I would be very pleased to hear of any potential solutions.
>
>
>
>Cheers,
>
>
>
>Jacqui.
>
>
>
>Jacqueline Ross
>Biomedical Imaging Research Unit
>School of Medical Sciences
>Faculty of Medical & Health Sciences
>The University of Auckland
>Private Bag 92019
>Auckland, NEW ZEALAND
>
>Tel: [phone] Ext 87438
>Fax: [phone]
>
>http://www.health.auckland.ac.nz/biru/
><http://www.health.auckland.ac.nz/biru/>
>
>

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John J. Bozzola, Ph.D., Director
I.M.A.G.E. (Integrated Microscopy & Graphics Expertise)
750 Communications Drive - MC 4402
Southern Illinois University
Carbondale, IL 62901  U.S.A.
Phone: [phone]
Email: [hidden email]
Web: http://www.siu.edu/~image/
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