OptimizeParams: Optimize Detection Params

Description Usage Arguments Details Value Author(s) References Examples

View source: R/all_functions_v8.R

Description

Optimize Detection Parameters for running a cell tracking job

Usage

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OptimizeParams(
  tc_obj,
  lnoise_range = NULL,
  min.px.diam = 5,
  diameter_range = NULL,
  threshold_range = NULL,
  target_cell_num = NULL,
  threads = 1,
  quantile.val = NULL,
  px.margin = NULL,
  plot = FALSE,
  verbose = FALSE,
  dryrun = FALSE
)

Arguments

tc_obj

a trackedCells object

lnoise_range

numeric vector of lnoise values to be used in the optimization step. Can be NULL

min.px.diam

integer, minimum diameter of a particle (cell). Particles with a diameter smaller than min.px.diam are discarded

diameter_range

numeric vector of diameter values to be used in the optimization step. Can be NULL

threshold_range

numeric vector of threshold values to be used in the optimization step. Can be NULL

target_cell_num

integer, the expected (optimal) number of cells to be detected in each frame

threads

integer, number of cores to use for parallelization

quantile.val

numeric, argument passed to EstimateDiameterRange(). If NULL, it is defaulted to 0.99

px.margin

numeric, argument passed to EstimateDiameterRange(). If NULL, it ia defaulted to 2

plot

if 'TRUE', plots results in the end

verbose

shall information about the progress of the operation be printed to screen/console

dryrun

shall a dryrun be performed

Details

The lnoise param is used to guide a lowpass blurring operation, while the lobject param is used to guide a highpass background subtraction. The threshold param is used for a background correction following the initial image convolution

Value

a trackedCells object

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 <- OptimizeParams(tc_obj = x, lnoise_range = c(5,7,10),
                    diameter_range = c(12,14,18),
                    threshold_range = c(4,7), dryrun = TRUE)
getOptimizedParameters(x)

ocbe-uio/CellMigRation documentation built on Dec. 26, 2021, 10:19 p.m.