CentroidValidation: Validate Centroids

Description Usage Arguments Value Author(s) References Examples

View source: R/all_functions_v8.R

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

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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, damiano.fantini@gmail.com

References

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

Examples

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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. 26, 2021, 10:19 p.m.