How to reduce brightness of ceratin pixels from an Image?

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Dongyu Liang 2021-2-2

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评论： Dongyu Liang 2021-2-4

Hi,

I have a set of particle micro-CT images for 3D structure generation. However, the ash on the particle cause pixels to be super brightness and brings negative effect on threshold value selection for segmentation. The basic idea is to set a value of brightness to be a threshold value, any higher brightness value of each pixel will be reduced to a lower brightness value. But how to appropriate determine those brightness values is a problem. Is there any methods or functions in Matlab can solve this problem?

Thanks!

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Answer 1

Bjorn Gustavsson 2021-2-2

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Is this the operation that you're asking for?

too_bright = 123; % or your chosen level
replacement_level = 123; % Not a good idea to give it a lower value, you might want a nan to flag pixels as bad?
Im(Im(:)>too_bright) = replacement_level;

Where Im is your image.

HTH

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Bjorn Gustavsson 2021-2-3

What are your original images? Are they slices of a 3D-tomography of sorts? Or are they the images you or someone else will use for tomographic reconstruction?

If it is the latter definitely never ever use inpainting or any other "magicing up" of image information. Typically when solving inverse problems like CT we have problems with error and noise-propagation already with "perfect" observations. To come up with any ever so clever fake observations where your input data is corrupted is not the way to go, just follow Wittgesteins sound advice "Wovon man nicht sprechen kann, darüber muß man schweigen". If you have no good data from a pixel remove it from the processing, don't lie about what should've been there.

If you have slices that you're going to use for some sort of quantitative data analysis of the CT-ed object then do that with the good information, and still avoid to invent information that is not there, you be far more true to you observations if you learn to handle the outlier-problem.

If you have slices of some 3D-CT and want to display some pretty visualizations for show - then knock yourself out no-one is going to be bothered about it anyway, but know what you've done and what is what.

I don't know what Inpaint in matematica does, but "texture synthesis" is mentioned. I've seen that mentioned but Ḯve never bothered with that. There are a Poisson-type inpainting function on the file exchange, that I use: inpaint_nans.

HTH

Bjorn Gustavsson 2021-2-4

Well, if the ash-part is just a small super-bright part of the particles you want to identify, then by all means simply replace these outliers with nan and then use the inpaint_nans function to fill in those wholes. That should give you a non-toxic (for your processing) filling-in of your particles. Then the segmentation/identification should(ought to?) work OK. Just take extra care to check that nothing "peculiar" happens with the inpaint-threshold-identification sequence - I always think about this in terms of making a decision about radioteraphy on a brain-tumor, if I were to have done some inpainting type operation I'd like to be pretty darn sure about the advice I'd give (in my field the stakes are not that serious, but I assume that yours is...).

Dongyu Liang 2021-2-4

Thank you!

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