clumps: Find 3D aggregates/clumps

In Russel88/RCon3D: Analysis of Confocal Images of Microbial Biofilms

Find 3D aggregates/clumps

Description

Function to group adjacent pixels in aggregates/clumps

Usage

clumps(
  imgs,
  channels,
  kern.neighbour = c(3, 3, 3),
  type.neighbour = "box",
  kern.smooth = NULL,
  type.smooth = "box",
  layers = NULL,
  pwidth = NULL,
  zstep = NULL,
  naming = NULL,
  coords = FALSE,
  thresh = 0,
  points = NULL,
  cores = 1
)

Arguments

imgs	The paths of array files; i.e. output from loadIMG or findIMG functions.
channels	Name of the channel to find aggregates in. Should be in the names of the array files
kern.neighbour	Numeric vector indicating range of neighbouring pixels to aggregate in the x,y,z directions. Has to be odd intergers. c(1,1,1) means no aggregating.
type.neighbour	Type of kernel for neighbourhood. "box" includes diagonals, "diamond" is without diagonals
kern.smooth	Optional. Numeric vector indicating range of median smoothing in the x,y,z directions. Has to be odd integers. c(1,1,1) means no smoothing.
type.smooth	Optional. Type of kernel for smooth "box" includes diagonals, "diamond" is without diagonals
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
pwidth	Optional. Width of pixels in microns to calculate aggregate size in microns instead of pixels
zstep	Optional. z-step in microns to calculate aggregate size in microns instead of pixels
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
coords	Optional. Logical. Return coordinates of the centroids of each aggregate. This can be somewhat time-consuming if there are many aggregates
thresh	Optional. Numeric. Clumps containing fewer than this number of pixels are discarded. Default 0
points	Optional. List. 3D coordinates of points from which the distance to each aggregate should be calculated. The list should have an element for each image in imgs in the same order. Each element is a vector of length 3 with the coordinates. E.g. points = list(c(250,200,10),c(500,300,20))
cores	Integer. Number of cores to use for parallel computing.

Value

A list with two parts. First part is a dataframe with ID, size of aggregates in pixels, size of aggregates in microns if pwidth and zstep are provided, coordinates if coords is TRUE, if coords is TRUE also variables, Edge.x, Edge.y and Edge.z, indicating how many pixels of each aggregate is on the edge of the image, and name of image. Second part is a list of the arrays in which pixels are NA if empty or given a number indicating the aggregate ID

Russel88/RCon3D documentation built on Dec. 14, 2022, 11:06 p.m.