MaxContrastProjection

DOI: 10.18129/B9.bioc.MaxContrastProjection    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MaxContrastProjection.

Perform a maximum contrast projection of 3D images along the z-dimension into 2D

Bioconductor version: 3.9

A problem when recording 3D fluorescent microscopy images is how to properly present these results in 2D. Maximum intensity projections are a popular method to determine the focal plane of each pixel in the image. The problem with this approach, however, is that out-of-focus elements will still be visible, making edges and fine structures difficult to detect. This package aims to resolve this problem by using the contrast around a given pixel to determine the focal plane, allowing for a much cleaner structure detection than would be otherwise possible. For convenience, this package also contains functions to perform various other types of projections, including a maximum intensity projection.

Author: Jan Sauer, Bernd Fischer

Maintainer: Jan Sauer <jan.sauer at dkfz-heidelberg.de>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MaxContrastProjection")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MaxContrastProjection")

 

PDF	R Script	MaxContrastProjection
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, ImmunoOncology, Preprocessing, Software, Visualization
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	Artistic-2.0
Depends	R (>= 3.4)
Imports	EBImage, stats, methods
LinkingTo
Suggests	knitr, BiocStyle, testthat
SystemRequirements	GNU make
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MaxContrastProjection_1.8.0.tar.gz
Windows Binary	MaxContrastProjection_1.8.0.zip
Mac OS X 10.11 (El Capitan)	MaxContrastProjection_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MaxContrastProjection
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MaxContrastProjection
Package Short Url	https://bioconductor.org/packages/MaxContrastProjection/
Package Downloads Report	Download Stats