tiff_to_array: Make Array from .tif file(s)

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

Make Array from .tif file(s)

Description

Create an array from one or more .tif files. Looks for .tif in the working directory

Usage

tiff_to_array(channels, split, multi, multi.name)

Arguments

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. Not that multi indicates if the .tif files contains multiple 3D images, and split indicates if the .tif files contains multiple layers (z-direction). If split is TRUE, multi cannot be non-NULL.

Value

Arrays as RDS files in working directory

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