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 1

Outline  Introduction  Specialized Methods  Standard Methods  Experimental Results  Sensitivity to Noise  Conclusion 2

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 3

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

Outline  Introduction  Specialized Methods  Standard Methods  Experimental Results  Sensitivity to Noise  Conclusion 5

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 6

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 7

Outline  Introduction  Specialized Methods  Standard Methods  Experimental Results  Sensitivity to Noise  Conclusion 8

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 9

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 10

Standard Methods (Experimental Results) 11

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 12

Standard Methods ( Sensitivity to Noise) 13

Outline  Introduction  Specialized Methods  Standard Methods  Experimental Results  Sensitivity to Noise  Conclusion 14

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 15