EstimateDiameterRange: Detect Paricle Diameters in a Numeric matrix

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

Description

Estimates the diameters of particles in a numeric matrix

Usage

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, [e-mail]

References

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

Examples

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.