bpass: Perform a bandpass by convolving with an appropriate kernel

In ocbe-uio/cellmigRation: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics

Description

Implements a real-space bandpass filter that suppresses pixel noise and long-wavelength image variations while retaining information of a characteristic size. First, a lowpassed image is produced by convolving the original with a gaussian. Next, a second lowpassed image is produced by convolving the original with a boxcar function. By subtracting the boxcar version from the gaussian version, we are using the boxcar version to perform a highpass. This code 'bpass.pro' is copyright 1997, John C. Crocker and David G. Grier. It should be considered 'freeware'- and may be distributed freely in its original form when properly attributed.

Usage

bpass(image_array, lnoise, lobject = NULL, threshold)

Arguments

image_array	Numeric matrix corresponding to the image to be filtered
lnoise	Characteristic lengthscale of noise in pixels.
lobject	Integer length in pixels somewhat larger than a typical object
threshold	By default, after the convolution, any negative pixels are reset to 0. Threshold changes the threshhold for setting pixels to 0. Positive values may be useful for removing stray noise or small particles.

Value

Numeric matrix corresponding to the filtered image

Author(s)

Damiano Fantini, [e-mail]

References

https://www.data-pulse.com/dev_site/cellmigration/ https://www.mathworks.com/matlabcentral/fileexchange/60349-fasttracks

Examples

x0 <- cbind(
    c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
    c(0, 0, 0, 0, 0, 1, 1, 4, 2, 0, 0, 0, 0, 0, 0),
    c(0, 0, 0, 0, 1, 2, 6, 5, 3, 0, 0, 0, 1, 0, 0),
    c(0, 0, 0, 0, 5, 5, 6, 8, 6, 1, 0, 0, 6, 2, 0),
    c(0, 0, 2, 5, 8, 7, 3, 5, 1, 0, 0, 0, 6, 2, 0),
    c(0, 0, 1, 5, 8, 7, 4, 5, 2, 0, 0, 0, 0, 0, 0),
    c(0, 0, 0, 5, 8, 7, 4, 5, 2, 0, 0, 0, 0, 0, 0),
    c(0, 0, 0, 1, 4, 5, 2, 4, 0, 0, 0, 0, 0, 0, 0),
    c(0, 0, 0, 0, 2, 3, 2, 1, 0, 0, 0, 0, 0, 0, 0),
    c(0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0),
    c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 0),
    c(9, 9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 2, 1),
    c(2, 9, 9, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 2, 1),
    c(0, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0),
    c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0),
    c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0))
y0 <- cellmigRation:::bpass(x0, lnoise = 1, lobject = 5, threshold = 1)
par(mfrow = c(1, 2))
image(x0); title("original")
image(y0); title("after bpass")

ocbe-uio/cellmigRation documentation built on Dec. 16, 2021, 10:59 p.m.