quant: Quantifies the pixels in images

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

Quantifies the pixels in images

Description

Quantifies the number of pixels for each channel in any direction (default z-stack)

Usage

quant(imgs, channels, naming = NULL, cores = 1, axis = 3)

Arguments

imgs	The paths of array files; i.e. output from loadIMG or findIMG functions.
channels	Character vector with name(s) of channels. Channel names should be in the names of the array files
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
cores	Number of cores for parallel computing
axis	Axis to aggregate over (1: x, 2: y, 3:z). Default 3 (z-axis)

Value

A dataframe with number of pixels for each layer

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