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("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 | R Script | |
| Reference Manual | ||
| 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 |
| URL |
See More
| Suggests | knitr, BiocStyle, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| 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 |