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[R Pacakge]Introduction to EBImage [推广有奖]

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Nicolle 学生认证  发表于 2018-12-5 03:13:46 |显示全部楼层

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Introduction to EBImage.pdf (13.41 MB)



Introduction to EBImage
Andrzej Oleś, Gregoire Pau, Oleg Sklyar, Wolfgang Huber

30 October 2018
Abstract
EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.


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Nicolle 学生认证  发表于 2018-12-5 03:14:04 |显示全部楼层
  1. Getting started
  2. EBImage is an R package distributed as part of the Bioconductor project. To install the package, start R and enter:

  3. install.packages("BiocManager")
  4. BiocManager::install("EBImage")
  5. Once EBImage is installed, it can be loaded by the following command.

  6. library("EBImage")
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Nicolle 学生认证  发表于 2018-12-5 03:14:45 |显示全部楼层
2. Reading, displaying and writing images

  1. Basic EBImage functionality includes reading, writing, and displaying of images. Images are read using the function readImage, which takes as input a file name or an URL. To start off, let us load a sample picture distributed with the package.

  2. f = system.file("images", "sample.png", package="EBImage")
  3. img = readImage(f)
  4. EBImage currently supports three image file formats: jpeg, png and tiff. This list is complemented by the RBioFormats package providing support for a much wider range of file formats including proprietary microscopy image data and metadata.

  5. The image which we just loaded can be visualized by the function display.

  6. display(img, method="browser")
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Nicolle 学生认证  发表于 2018-12-5 03:18:24 |显示全部楼层
  1. 3 Image data representation
  2. #EBImage uses a package-specific class Image to store and process images. It extends the R base class array, and all EBImage functions can also be called directly on matrices and arrays. You can find out more about this class by typing ?Image. Let us peek into the internal structure of an Image object.

  3. str(img)

  4. #Image data can be accessed as a plain R array using the imageData accessor,

  5. imageData(img)[1:3, 1:6]

  6. #the as.array method can be used to coerce an Image to an array.

  7. is.Image( as.array(img) )

  8. #The distribution of pixel intensities can be plotted in a histogram, and their range inspected using the range function.

  9. hist(img)

  10. #A useful summary of Image objects is also provided by the show method, which is invoked if we simply type the object’s name.

  11. img

  12. #Have a closer look a our color image.

  13. print(imgcol, short=TRUE)
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ltan_ca 发表于 2018-12-5 05:17:21 |显示全部楼层
Thanks!!!!
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HappyAndy_Lo 发表于 2018-12-5 08:45:43 |显示全部楼层
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nieqiang110 发表于 2018-12-5 11:00:59 |显示全部楼层
[R Pacakge]Introduction to EBImage
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nieqiang110 发表于 2018-12-5 12:14:18 |显示全部楼层
不让安装啊
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nieqiang110 发表于 2018-12-5 12:14:37 |显示全部楼层
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'BiocVersion', 'EBImage'
Warning: unable to access index for repository https://bioconductor.org/packages/3.8/bioc/src/contrib:
  cannot open URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/PACKAGES'
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albertwishedu 发表于 2018-12-5 17:09:17 |显示全部楼层
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