image analysis using r2

7/29/2019 Image Analysis Using R2

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Chris Campbell

LondonR - 13th July 2010

Image Analysis Using R



Steps to image analysis• Image capture

• Clean image/reduce noise

• Extract information

• Analyze information



Image Capture

Light

Photography

Light microscopy

Fluorescence microscopy

gels

cells

tissue samples

http:// ... western blothttp:// ... cells



Image Capture

Light

Photography

Light microscopy


gels

cells

tissue samples

X-rayRadiography

Computed tomography (CT)

bones

tumours

http:// ... x-rayhttp:// ... cat scan



Image Capture

Light

Photography

Light microscopy


gels

cells

tissue samples

X-rayRadiography

Computed tomography

bones

tumours

Magnetism Magnetic resonance imaging (MRI) patients

http:// ... MRI



Image Capture

Light

Photography

Light microscopy


gels

cells

tissue samples

X-rayRadiography

Computed tomography

bones

tumours

Magnetism Magnetic resonance imaging patients

ElectronsScanning electron microscopy

Transmission electron microscopy

insects

viruses

http:// ... SEM insecthttp:// ... TEM virus



Image Capture

Light

Photography

Light microscopy


gels

cells

tissue samples

X-rayRadiography

Computed tomography

bones

tumours




insects

viruses

PositronsPositron emission tomography

(PET)

tumours

http:// ... positron emission tomography



Image Capture

Light

Photography

Light microscopy


gels

cells

tissue samples

X-rayRadiography

Computed tomography

bones

tumours




insects

viruses

PositronsPositron emission tomography

(PET)

tumours

Intermolecular

forces

Atomic force microscopy inorganic surfaceshttp://pico.iis.u-tokyo.ac.jp/media/16/20060621-QuenchedSi-AFM.jpg

http://pico.iis.u-tokyo.ac.jp/media/16/20060621-QuenchedSi-AFM.jpg











Generally… • Use large numbers of images

• Use all images

• Use whole image, not crop

• Random selection not "typical region"

• i.e. avoid subjectivity



Image Processing Libraries in CRANbiOps Image processing and analysis

dcemri A Package for Medical Image Analysis

dpmixsim Dirichlet Process Mixture model simulation for clustering & image segmentation

edci Edge Detection and Clustering in Images

epsi Edge Preserving Smoothing for Images

FITSio FITS (Flexible Image Transport System) utilities

PET Simulation and Reconstruction of PET Images

R4dfp 4dfp MRI Image Read & Write Routines

rimage Image Processing Module for R

RImageJ R bindings for ImageJ

ripa R Image Processing & Analysis

tractor.base A package for reading, manipulating & visualising magnetic resonance images

adimpro Adaptive Smoothing of Digital Images



Libraries in CRANbiOps Image processing and analysis

dcemri A Package for Medical Image Analysis

dpmixsim Dirichlet Process Mixture model simulation for clustering & image segmentation

edci Edge Detection and Clustering in Images

epsi Edge Preserving Smoothing for Images

FITSio FITS (Flexible Image Transport System) utilities

PET Simulation and Reconstruction of PET Images

R4dfp 4dfp MRI Image Read & Write Routines

rimage Image Processing Module for R

RImageJ R bindings for ImageJ

ripa R Image Processing & Analysis

tractor.base A package for reading, manipulating & visualising magnetic resonance images

adimpro Adaptive Smoothing of Digital Images



• Open source

• Java

• Image analysis software http://rsbweb.nih.gov/ij/

package:RImageJ• Authors: Romain Francois & Philippe Grosjean

• Bindings between R and ImageJ

http://rsbweb.nih.gov/ij/

http://rsbweb.nih.gov/ij/



Subjectivity vs. Objectivity• Hypothesis: blue blobs are always larger than yellow blobs



Subjectivity• Hypothesis: blue blobs are always larger than yellow blobs

Manualmeasurements




It’s easy to accept

manualmeasurements

when they makesense, but it’s

tempting torepeat them if they seem wrong




Subjectiveobserver acceptsexpected

hypothesis



Objectivity• Hypothesis: blue blobs are always larger than yellow blobs

Automaticallythreshold



Objectivity• Hypothesis: blue blobs are always larger than yellow blobs

Objective observer automates analysisand rejects

hypothesis



Automate Procedures• Identify objects without making subjective decisions



Run ImageJ from R• Open connection to

an image

• Use IJ$run() to

access macros

• Great potential for

automating image

processing from R



Run ImageJ from R• However, some key macros not yet implemented

(e.g. setAutoThreshold, imageCalculator)



package:rimage• Author: Nikon

• Reads jpegs into

RGB arrays

• Plot function defined

for objects of class

"imagematrix"



Analyze information• Plots and statistical summaries of particles from image

Single image

Multiple images



Conclusions• Images available?

• Ensure quality/validate method

• Choose useful measures

• Use analysis to make predictions



Acknowledgements• Mango Solutions www.mango-solutions.com

• L. R. Contreras-Rojas, R. H. Guy

http://www.bath.ac.uk/pharmacy/staff/rhg.html

• NAPOLEON http://www.ehu.es/napoleon/

http://www.mango-solutions.com/


http://www.ehu.es/napoleon/

http://www.ehu.es/napoleon/





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