occupancy: 3D Occupancy
In Russel88/RCon3D: Analysis of Confocal Images of Microbial Biofilms

occupancy

R Documentation

3D Occupancy

Description

Function to calculate the occupancy of a target channel at certain distances from a focal channel

Usage

occupancy(
  imgs,
  focal.channel,
  target.channel,
  size,
  npixel,
  R = 10,
  dstep = 1,
  pwidth,
  zstep,
  cores = 1,
  kern.smooth = NULL,
  layers = NULL,
  naming = NULL
)

occupancy.default(
  imgs,
  focal.channel,
  target.channel,
  size,
  npixel,
  dstep = 1,
  pwidth,
  zstep,
  cores = 1,
  kern.smooth = NULL,
  layers = NULL,
  naming = NULL
)

Arguments

`imgs`	The paths of array files; i.e. output from `loadIMG` or `findIMG` functions.
`focal.channel`	Name of the channel from which the distance is calculated. Should be in the names of the array files
`target.channel`	Name of the channel for calculate occupancy of. Should be in the names of the array files
`size`	The maximum distance (microns) to examine. Has to be a multiple of both pwidth and zstep. Beware, increasing size will increase runtime exponetially!
`npixel`	Number of random pixels to examine. Increasing this will increase precision (and runtime in a linear fashion)
`R`	Number of times to run the occupancy analysis
`dstep`	The interval between examined distances (microns). Increasing this decreases resolution but speeds up function linearly. Defaults to 1
`pwidth`	Width of pixels in microns
`zstep`	z-step in microns
`cores`	The number of cores to use. Defaults to 1
`kern.smooth`	Optional. Numeric vector indicating range of median smoothing in the x,y,z directions. Has to be odd intergers. c(1,1,1) means no smoothing.
`layers`	Optional. Should the function only look in a subset of layers. A list with lists of layers to use for each image. Can also be the output from `extract_layers`
`naming`	Optional. Add metadata to the output dataframe by looking through names of array files. Should be a list of character vectors, each list element will be added as a variable. Example: naming=list(Time=c("T0","T1","T2")). The function inserts a variable called Time, and then looks through the names of the array files and inserts characters mathcing either T0, T1 or T2