MaxContrastProjection

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last 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>

Citation (from within R, enter citation("MaxContrastProjection")):

Installation

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


if (!require("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")
MaxContrastProjection PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, ImmunoOncology, Preprocessing, Software, Visualization
Version 1.8.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License Artistic-2.0
Depends R (>= 3.4)
Imports EBImage, stats, methods
System Requirements GNU make
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Suggests knitr, BiocStyle, testthat
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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
Bioc Package Browser https://code.bioconductor.org/browse/MaxContrastProjection/
Package Short Url https://bioconductor.org/packages/MaxContrastProjection/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive