CentroidArray: Build a Centroid Array

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

Description

Create an array containing centroid data for particles identified in each frame of the imported TIFF image stack

Usage

CentroidArray(stack, lobject, threshold, dryrun = FALSE)

Arguments

stack	3D matrix loaded to workspace from .tif stack
lobject	Integer length in pixels somewhat larger than a typical object
threshold	the minimum brightness of a pixel that might be local maxima
dryrun	logical, shall the execution be skipped

Value

data.frame of centroids, with 4 columns corresponding to x-position of centroid, y-postion of centroid, brightness, and square of the radius of gyration

Author(s)

Damiano Fantini, [e-mail]

References

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

Examples

# by default, the dryrun argument is set to FALSE
df <- get(data(TrackCellsDataset))
x0 <- getCellImages(df)
y0 <- cellmigRation:::CentroidArray(x0, 16, 10, TRUE)
y0

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