coscore: Colocalization Coefficients

In kuwisdelu/matter: Out-of-core statistical computing and signal processing

Colocalization Coefficients

Description

Compute Manders overlap coefficient (MOC), and Manders colocalization coefficients (M1 and M2), and Dice similarity coefficient.

Usage

coscore(x, y, threshold = NA)

Arguments

x, y	Images to be compared. These can be numeric or logical. If numeric, then the "overlap" is defined where both images are nonzero.
threshold	The intensity threshold to use when comparing the images. If NA, this will be determined automatically from the technique described in Costes et al. (2004). Alternatively, this can be a function such as median that can be applied to return a suitable threshold.

Details

The Dice coefficient and Manders overlap coefficient are symmetric between images, while M1 and M2 measure the overlap relative to x and y respectively.

Value

A numeric vector with elements named "MOC", "M1", "M2", and "Dice", and an attribute named "threshold" giving the numeric thresholds (if applicable) for converting each image to a logical mask.

Author(s)

Kylie A. Bemis

References

K. W. Dunn, M. M. Kamocka, and J. H. McDonald. “A practical guide to evaluating colocalization in biological microscop.” American Journal of Physiology: Cell Physiology, vol. 300, no. 4, pp. C732-C742, 2011.

S. V. Costes, D. Daelemans, E. H. Cho, Z. Dobbin, G. Pavlakis, and S. Lockett. “Automatic and Quantitative Measurement of Protein-Protein Colocalization in Live Cells.” Biophysical Journal, vol. 86, no. 6, pp. 3993-4003, 2004.

K. H. Zou, S. K. Warfield, A. Bharatha, C. M. C. Tempany, M. R. Kaus, S. J. Haker, W. M. Wells, III, F. A. Jolesz, and R. Kikinis. “Statistical Validation of Image Segmentation Quality Based on a Spatial Overlap Index.” Academic Radiology, vol. 11, issue 2, pp. 178-189, 2004.

Examples

set.seed(1)
y <- x <- matrix(0, nrow=32, ncol=32)
x[5:16,5:16] <- 1
x[17:28,17:28] <- 1
x <- x + runif(length(x))
y[4:15,4:15] <- 1
y[18:29,18:29] <- 1
y <- y + runif(length(y))
xl <- x > median(x)
yl <- y > median(y)

coscore(x, x)
coscore(x, y)
coscore(x, y, threshold=median)
coscore(xl, yl)

kuwisdelu/matter documentation built on Dec. 8, 2024, 8:09 p.m.