Prep4OptimizeParams: Prepare For Parameter Optimization

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

Description

Pre-processing as part of the Optimization Parameter process

Usage

Prep4OptimizeParams(
  stack_img,
  lnoise_range = NULL,
  min.px.diam = 5,
  diameter_range = NULL,
  threshold_range = NULL,
  target_cell_num = NULL,
  quantile.val = NULL,
  px.margin = NULL,
  plot = FALSE,
  verbose = FALSE
)

Arguments

stack_img	input image
lnoise_range	numeric, lnoise values to test
min.px.diam	numeric, minimum number of pixels of a cell signal
diameter_range	numeric, numeric values for diameter
threshold_range	numeric, numeric values for threshold
target_cell_num	numeric, target number of cells, can be NULL
quantile.val	numeric, the quantile prob used to suppress noise
px.margin	numeric, the frame margin size
plot	logical, shall a plot be printed
verbose	logical, shall info be printed to console

Details

This is an internal function supporting the Optimization Parameter steps

Value

a data frame of combined parameters to be tested

Examples

x <- get(data(TrackCellsDataset))
x <- cellmigRation::getCellImages(x = x)
y <- cellmigRation:::Prep4OptimizeParams(stack_img = x)
y$success

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