EstimateDiameterRange: Detect Paricle Diameters in a Numeric matrix

Description Usage Arguments Value Author(s) References Examples

View source: R/all_functions_v8.R

Description

Estimates the diameters of particles in a numeric matrix

Usage

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EstimateDiameterRange(
  x,
  px.margin = 2,
  min.px.diam = 5,
  quantile.val = 0.99,
  plot = TRUE
)

Arguments

x

numeric matrix corresponding to a digital image

px.margin

integer, number of pixels used as margin while searching/filtering for neighboring particles

min.px.diam

integer, minimum diameter of a particle (cell). Particles with a diameter smaller than min.px.diam are discarded

quantile.val

numeric, must be bigger than 0 and smaller than 1. Quantile for discriminating signal and background; only pixels with intensity higher than the corresponding quantile will count as signal while estimating particle diameters

plot

logial, shall a histogram of the distribution of diameters be shown

Value

list including summary stats and data about the particles found in the image

Author(s)

Damiano Fantini, damiano.fantini@gmail.com

References

https://www.data-pulse.com/dev_site/cellmigration/

Examples

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a <- cbind(c(1, 1, 1, 0, 0, 0, 0, 0, 1, 1),
           c(1, 1, 0, 0, 0, 0, 0, 0, 1, 1),
           c(1, 0, 0, 0, 0, 0, 0, 0, 0, 0),
           c(0, 0, 0, 0, 1, 1, 0, 0, 0, 0),
           c(0, 0, 0, 1, 1, 1, 0, 0, 0, 0))
graphics::image(a)
b <- EstimateDiameterRange(a, min.px.diam = 2)
print(b$estim.cell.num)
print(b$raw)

ocbe-uio/CellMigRation documentation built on Dec. 26, 2021, 10:19 p.m.