CentroidValidation: Validate Centroids

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

Description

Validate parameters used to identify cells in a image stack. A figure containing current image frame with identified particles labeled with circles and numerical tags is generated. This function is included for consistency and compatibility reasons with the original fastTracks software (Matlab). Also, consider using VisualizeStackCentroids() or visualizeCellTracks() instead.

Usage

CentroidValidation(
  stack,
  slice,
  lobject,
  threshold,
  pnt.cex = 1.2,
  txt.cex = 0.85,
  offset = 0.18
)

Arguments

stack	stack of images to be evaluated
slice	index of the frame within the stack to be evaluated
lobject	integer, length in pixels somewhat larger than a typical object (cell)
threshold	the minimum brightness of a pixel that might be local maxima. NOTE: Make it big and the code runs faster but you might miss some particles. Make it small and you'll get everything and it'll be slow.
pnt.cex	cex of the circle drawn around each cell
txt.cex	cex of the text used for annotating cells
offset	offset used for annotating cells

Value

data.frame of centroid positions

Author(s)

Damiano Fantini, [e-mail]

References

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

Examples

x <- get(data(TrackCellsDataset))
x <- getCellImages(x)
x$images[[1]] <- x$images[[1]][seq(110,160,by=1), seq(100,160,by=1)]
cellmigRation:::CentroidValidation(x, slice = 1, lobject =10, threshold = 5)

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