loadIMG: Load .tif images into R

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

Load .tif images into R

Description

Create an array from one or more .tif files.

Usage

loadIMG(path, channels, split = FALSE, multi = NULL, multi.name = NULL)

Arguments

path	The path of either a folder with all .tif files to be loaded (if split=FALSE), or a folder where each image is in a separate subfolder with all z-stacks and channels in that folder (if split=TRUE)
channels	Character vector with name(s) of channels. Channel names should be in the names of the .tif files
split	Logical indicating if all z-stacks are in one .tif (FALSE) or in a folder with a .tif for each z-stack (TRUE)
multi	Integer. If the .tif contains multiple images this varible should indicate how to divide them up. Three images, each composed of 50, 100, and 150 layers: c(50,100,150). 10 images with each 50 layers. rep(50, 10). If NULL input is assumed to be a single 3D image
multi.name	If multi is not NULL, a vector with names for images.

Details

If the .tif file has a color.space attribute saying "white is zero" (and split=FALSE) the binary coding of the image is reversed

Value

Creates arrays as RDS files in the set path, and outputs the paths for these files

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