MATLAB: Image processing of confocal images (flattening)

confocalflatenningimage processing

Hi all,
I need help, I am new in matlab.
I need to done threshold of confocal images but problem is that I have to process them first because they are not well taken; sample was liquid and there is some konvex mistake, edges (somewhwre and half of image) of images are darker and not in same level (height) as a middle of image, so with pure threshold I cant get relevat datas (I have big number of images to process)of surface coverage. I need to get a flat picture of sample on same height as a middle of sample.
I have Matlab, not image processing toolbox. I am interested is it possible, and how this kind of image processing?
here are links for two of my images
http://img813.imageshack.us/i/testt.gif/
<http://www.uploadhouse.com/viewfile.php?id=9395381&PHPSESSID=2c010f135dc2fe8a05537baf4deefed4>

Best Answer

I think this is quite difficult. There seem to be two problems with the images: one is the defocusing; the other is the change in illumination (especially visible in the second image).
I am not sure how to deal with the change in focus, but anyway what to do depends on exactly what you need to measure. It may be that the lack of sharpness in part of the image is not a problem, if, for example, you just need to estimate the area of the darker structures. It is possible that deconvolution techniques may be some help, and if the blurring is a major problem then you could investigate that.
The gradient in illumination is easier to deal with, using adaptive thresholding. There's a file exchange contribution which might be applicable, and also a relevant demo with the Image Processing Toolbox.
Try fixing the illumination problems first, and then assess how much the blurring matters. What you do then depends on what exactly you need to get out of the images.
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