CellTracker: Compute Cell Tracks

Description Usage Arguments Details Value Author(s) References Examples

View source: R/all_functions_v8.R

Description

Analyze Stacks, detect cells in each frame, and analyze cell tracks over time

Usage

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CellTracker(
  tc_obj,
  import_optiParam_from = NULL,
  min_frames_per_cell = 1,
  lnoise = NULL,
  diameter = NULL,
  threshold = NULL,
  maxDisp = NULL,
  memory_b = 0,
  goodenough = 0,
  threads = 1,
  show_plots = FALSE,
  verbose = FALSE,
  dryrun = FALSE
)

Arguments

tc_obj

a trackedCells object.

import_optiParam_from

a trackedCells object (optional) used to import optimized parameters; can be NULL.

min_frames_per_cell

numeric, minimum number of consecutive frames in which a cell shall be found in order to retain that cell in the final cell tracks data.frame. Defaults to 1.

lnoise

numeric, lnoise parameter; can be NULL if OptimizeParams() has already been run

diameter

numeric, diameter parameter; can be NULL if OptimizeParams() has already been run

threshold

numeric, threshold parameter; can be NULL if OptimizeParams() has already been run

maxDisp

numeric, maximum displacement of a cell per time interval. When many cells are detected in each frame, small maxDisp values should be used.

memory_b

numeric, memory_b parameter as used in the original track.m function. In the current R implementation, only the value memory_b=0 is accepted

goodenough

numeric, goodenough parameter as used in the original track.m function. In the current R implementation, only the value goodenough=0 is accepted

threads

integer, number of cores to use for parallelization

show_plots

logical, shall cells detected in each frame of the image stack be visualized

verbose

logical, shall info about the progress of the cell tracking job be printed

dryrun

logical, 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 <- CellTracker(x, dryrun=TRUE)
getTracks(x)[seq(1,12,by=1),]

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