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On the Use of Standards for Microarray Lossless Image Compression

On the Use of Standards for Microarray Lossless Image Compression. Author :Armando J. Pinho*, Antonio R. C.Paiva, and Antonio J. R. Neves Source :IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING,VOL.53, NO. 3, MARCH 2006 Speaker: Ren-Li Shen. Outline. Introduction

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On the Use of Standards for Microarray Lossless Image Compression

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  1. On the Use of Standards for Microarray Lossless ImageCompression Author :Armando J. Pinho*, Antonio R. C.Paiva, and Antonio J. R. Neves Source :IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING,VOL.53, NO. 3, MARCH 2006 Speaker: Ren-Li Shen

  2. Outline • Introduction • Specialized Methods • Standard Methods • Experimental Results • Sensitivity to Noise • Conclusion

  3. Introduction • Standard image coding techniques applied to the lossless compression of microarray images • JPEG2000 • JBIG • JPEG-LS • Try to overcome some of the drawbacks • Image sources

  4. Introduction • Trying to identify compression technologies • Provide efficient lossless compression results • Offer relevant features for the microarray image compression problem

  5. Outline • Introduction • Specialized Methods • Standard Methods • Experimental Results • Sensitivity to Noise • Conclusion

  6. Specialized Methods • Four published methods • Jornsten et al. • Gridding and segmentation • Using a low complexity lossless compression algorithm • SLOCO • Hua et al. • Transform-based coding technique • Segmentation is using the Mann-Whitney algorithm • Separately spots and background

  7. Specialized Methods • Faramarzpour et al. • Locating and extracting the microarray spots • Transforming the ROI(region of interest) into an one-dimensional signal • Lonardi et al. • Lossless and lossy compression algorithms for microarray images • Fully automatic gridding procedure • Similar to Faramarzpour’s method • Split into two channels • Foreground • Background

  8. Outline • Introduction • Specialized Methods • Standard Methods • Experimental Results • Sensitivity to Noise • Conclusion

  9. Standard Methods • JBIG • Context-based arithmetic coding • Focused on bi-level imagery • JPEG-LS • Predictive coding • Lossless compression of continuous-tone images • JPEG2000 • Transform based • Providing a wide range of functionalities

  10. Standard Methods(Experimental Results) • Three different publicly available sources • Apo AI set (32) • ISREC set (14) • MicroZip (3) • Image size ranges from 1000 × 1000 to 5496 × 1956 pixels

  11. Standard Methods(Experimental Results)

  12. Standard Methods(Sensitivity to Noise) • 8bit-planes of cDNA microarray images are close to random and incompressible • Result in some degradation in the compression performance • Separated the images • 8bit-planes • 16bit-planes

  13. Standard Methods(Sensitivity to Noise)

  14. Outline • Introduction • Specialized Methods • Standard Methods • Experimental Results • Sensitivity to Noise • Conclusion

  15. Conclusion JPEG-LS gives the best lossless compression performance JBIG was consistently better than JPEG2000 The future of microarray image compression depends on special-purpose

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