CellTracker: Compute Cell Tracks

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

Description

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

Usage

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

• lnoise: Characteristic lengthscale of noise in pixels. Additive noise averaged over this length should vanish. May assume any positive floating value. May be also set to 0, in which case only the highpass "background subtraction" operation is performed.

• lobject Integer length in pixels somewhat larger than a typical object. Can also be set to 0, in which case only the lowpass "blurring" operation defined by lnoise is done without the background subtraction defined by lobject

• threshold Numeric. By default, after the convolution, any negative pixels are reset to 0. Threshold changes the threshhold for setting pixels to 0. Positive values may be useful for removing stray noise or small particles.

Value

a trackedCells object

Author(s)

Damiano Fantini, [e-mail]

References

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

Examples

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

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