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Image Analysis Using R

Image Analysis Using R. Chris Campbell LondonR - 13th July 2010. Steps to image analysis. Image capture Clean image/reduce noise Extract information Analyze information. Image Capture. http:// ... western blot http:// ... cells. Image Capture. http:// ... x-ray http:// ... cat scan.

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Image Analysis Using R

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  1. Image Analysis Using R Chris Campbell LondonR - 13th July 2010

  2. Steps to image analysis Image capture Clean image/reduce noise Extract information Analyze information

  3. Image Capture http:// ... western blot http:// ... cells

  4. Image Capture http:// ... x-ray http:// ... cat scan

  5. Image Capture http:// ... MRI

  6. Image Capture http:// ... SEM insect http:// ... TEM virus

  7. Image Capture http:// ... positron emission tomography

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

  9. Generally… • Use large numbers of images • Use all images • Use whole image, not crop • Random selection not "typical region" • i.e. avoid subjectivity

  10. Image Processing Libraries in CRAN

  11. Libraries in CRAN

  12. package:RImageJ • Authors: Romain Francois & Philippe Grosjean • Bindings between R and ImageJ • Open source • Java • Image analysis software http://rsbweb.nih.gov/ij/

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

  14. Subjectivity Hypothesis: blue blobs are always larger than yellow blobs Manual measurements

  15. Subjectivity Hypothesis: blue blobs are always larger than yellow blobs It’s easy to accept manual measurements when they make sense, but it’s tempting to repeat them if they seem wrong

  16. Subjectivity Hypothesis: blue blobs are always larger than yellow blobs Subjective observer accepts expected hypothesis

  17. Objectivity Hypothesis: blue blobs are always larger than yellow blobs Automatically threshold

  18. Objectivity Hypothesis: blue blobs are always larger than yellow blobs Objective observer automates analysis and rejects hypothesis

  19. Automate Procedures Identify objects without making subjective decisions

  20. Run ImageJ from R • Open connection to an image • Use IJ$run() to access macros • Great potential for automating image processing from R

  21. Run ImageJ from R However, some key macros not yet implemented (e.g. setAutoThreshold, imageCalculator)

  22. package:rimage Author: Nikon Reads jpegs into RGB arrays Plot function defined for objects of class "imagematrix"

  23. Analyze information Plots and statistical summaries of particles from image Single image Multiple images

  24. Conclusions Images available? Ensure quality/validate method Choose useful measures Use analysis to make predictions

  25. 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/

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