1. 11/29/2015 1 Image Processing

2. 11/29/2015 2 Systems and Software Image file formats Image processing applications

3. 11/29/2015 3 Image file formats Pixel images Graphic images Composite image files Images in manuscripts Graphic

4. 11/29/2015 4 Format issues Color, monochrome Capability –Gray value –Graphics –Calibration: size, sensitometry, etc... Compatibility Compression

5. 11/29/2015 5 Common formats TIFF –Common usage –Versatile: pixel, calibration –Pixel-based regions –Dialects Raw EPS –versatile –primarily, printed document format PICT, PICS –well developed standard –pixel and graphic format –primarily Macintosh

6. 11/29/2015 6 Common formats (more) DICOM –used in medical imaging Graphic arts: –MPEG, JPEG, GIF Import menu in NIH Image

7. 11/29/2015 7 Image processing software functions Image acquisition Image processing Quantitative data extraction Annotation and editing Database management File format conversion

8. 11/29/2015 8 Image processing software structure Task-dedicated General purpose Scripting/macro language

9. 11/29/2015 9 Software package examples NIH Image –http://rsb.info.nih.gov/nih-image/ Adobe Photoshop

10. 11/29/2015 10 Examples NIH Image & file conversion Annotation Copying, pasting

11. 11/29/2015 11 Software selection issues Compatibility with computer Functionality –Control of acquisition hardware (compatibility) –Range of processing algorithms Productivity

12. 11/29/2015 12 Image processing Contrast manipulation and enhancement Dyadic operation Image filtering Regions and region operation Image analysis

13. 11/29/2015 13 Monadic (one picture) operations Contrast manipulation and enhancement LUT operation –brightness, contrast –False color Gray value remap (apply LUT) Arithmetic operations Scale and rotate (also morphing) Other single image operations

14. 11/29/2015 14 Monadic operations Profile plot (and projection) Gray value histogram

15. 11/29/2015 15 Display operations Gray scale manipulation False color manipulation Enlarge, contract, scale to fit window See Adobe Illustrator for image editing

16. 11/29/2015 16 Example of rotation (a)(b)(c) (a) Original image, (b) rotated by 1.2°, nearest neighbor interpolation, (c) rotated by 1.2 °, bilinear interpolation.

17. 11/29/2015 17 Examples of histograms

18. 11/29/2015 18 Dyadic (two image) operations Dyadic (two variable) function: Examples: addition, multiplication, subtraction, and division. Problem: finite numerical range fro picture gray value leads to roundoff.

19. 11/29/2015 19 Example: shading correction

20. 11/29/2015 20 Image Filtering Convolution Rank filtering Edge detection

21. 11/29/2015 21 Image filtering (conceptual)

22. 11/29/2015 22 Convolution with the Fourier transform

23. 11/29/2015 23 Examples of linear filters Low-pass (smooth, Gauss) High-pass (sharpen, Mexican Hat, DOG) Shadow First derivative (shadow, find edges)

24. 11/29/2015 24 Example of smoothing Smoothing (5 times) BeforeAfter

25. 11/29/2015 25 Convolve Original Gauss (7x7) ‘Mexican hat’(17x17) Grad N Grad W

26. 11/29/2015 26 Nonlinear filters Median (noise eliminate and enhance) Minimum (erode) Maximum (dilate) Open Close

27. 11/29/2015 27 Example of morphological (rank) filters Opening (3) Closing (3) Original Minimum, erode (1) Maximum, dilate (1)

28. 11/29/2015 28 Example, grain counting Grain imageMaximum (5) Difference

29. 11/29/2015 29 Regions and region operation Thresholding, density slicing Erosion, dilation (rank filtering) Skeletons

30. 11/29/2015 30 Image analysis Sensitometric Geometric Categorical (image recognition)

31. 11/29/2015 31 Segmentation Geometrical shapes Interactive (outlining) Thresholding Filling

32. 11/29/2015 32 Segmentation - connected area Density slice, then use wand (auto-outline) to trace outline. Outline written on image with ‘draw boundary’ command.

33. 11/29/2015 33 Region of interest (ROI) analysis Area Perimeter Shape Average value Standard deviation

34. 11/29/2015 34 Example of measurement 126.00 132.48 39.27 14.37 11.16 AreaMeanLengthMinorMajor

35. 11/29/2015 35 Summary Paradigm: scanning, preprocessing, analysis Success depends on all parts of analysis chain Quality control –Quantitative evaluation of performance –Test samples –Repeated analysis

36. 11/29/2015 36 Summary Digital image acquisition - physical data to numbers Control of accuracy Experimental design Experimental preparation Scanner Scanner in the lab Complex device, operation and maintenance Quality control mandatory

37. 11/29/2015 37 Houston, we have a problem.