wsaPreProcessing: Data preprocessing for wound scratch assay (WSA).

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

Description

This function allows filtering of cells and preprocessing of the trajectory data from wound scratch assay (WSA) experiments.

Usage

wsaPreProcessing(
  object,
  PixelSize = 1.24,
  TimeInterval = 10,
  FrameN = NULL,
  imageH = 1500,
  woundH = 600,
  upperE = 400,
  lowerE = 1000,
  mar = 75,
  clearW = TRUE,
  ExpName = NULL
)

Arguments

object	CellMig class object.
PixelSize	A numeric value of the physical size of a pixel.
TimeInterval	A numeric value of the time elapsed between successive frames in the time-lapse stack.
FrameN	A numeric value of the number of frames. Default is NULL
imageH	A numeric value of the image height.
woundH	A numeric value of the image height.
upperE	A numeric value of the upper edge of the wound.
lowerE	A numeric value of the lower edge of the wound.
mar	A numeric value of the margin to be used to narrow the clearing zone inside the zone.
clearW	A logical vector that allows removing the cells within the wound. Default is TRUE.
ExpName	string, name of the experiment. Can be NULL

Value

An CellMig class object with filtered, annotated and preprocessed data.

Author(s)

Salim Ghannoum [e-mail]

References

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

Examples

WSADataset <- get(data(WSADataset))
wasDF=WSADataset[seq(1,30,by=1),]
wsaTD <- CellMig(wasDF)
wsaTD <- wsaPreProcessing(wsaTD,FrameN=20)

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