Gaussian smoothing of cv::Mat column

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Have you simply tried cv::GaussianBlur yet?

http://docs.opencv.org/modules/imgproc/doc/filtering.html?highlight=gaussianblur#gaussianblur

No, I thought this would work only for images... Im trying to pass each column seperately into cv::GaussianBlur, but how to find out ksize and sigma?

You determine the ksize and sigma. Maybe try Size(2,2) and 1.

It does not work. Should the ksize be also a single column?

My answer didnt make sense at all :D The kernel always has to be odd since you need a center point in your kernel to calculate the new value. If you have 2x2 you have no center . So size should be Size(3,3).