11/29/ Image Processing
11/29/ Systems and Software Image file formats Image processing applications
11/29/ Image file formats Pixel images Graphic images Composite image files Images in manuscripts Graphic
11/29/ Format issues Color, monochrome Capability –Gray value –Graphics –Calibration: size, sensitometry, etc... Compatibility Compression
11/29/ 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
11/29/ Common formats (more) DICOM –used in medical imaging Graphic arts: –MPEG, JPEG, GIF Import menu in NIH Image
11/29/ Image processing software functions Image acquisition Image processing Quantitative data extraction Annotation and editing Database management File format conversion
11/29/ Image processing software structure Task-dedicated General purpose Scripting/macro language
11/29/ Software package examples NIH Image – Adobe Photoshop
11/29/ Examples NIH Image & file conversion Annotation Copying, pasting
11/29/ Software selection issues Compatibility with computer Functionality –Control of acquisition hardware (compatibility) –Range of processing algorithms Productivity
11/29/ Image processing Contrast manipulation and enhancement Dyadic operation Image filtering Regions and region operation Image analysis
11/29/ 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
11/29/ Monadic operations Profile plot (and projection) Gray value histogram
11/29/ Display operations Gray scale manipulation False color manipulation Enlarge, contract, scale to fit window See Adobe Illustrator for image editing
11/29/ Example of rotation (a)(b)(c) (a) Original image, (b) rotated by 1.2°, nearest neighbor interpolation, (c) rotated by 1.2 °, bilinear interpolation.
11/29/ Examples of histograms
11/29/ 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.
11/29/ Example: shading correction
11/29/ Image Filtering Convolution Rank filtering Edge detection
11/29/ Image filtering (conceptual)
11/29/ Convolution with the Fourier transform
11/29/ Examples of linear filters Low-pass (smooth, Gauss) High-pass (sharpen, Mexican Hat, DOG) Shadow First derivative (shadow, find edges)
11/29/ Example of smoothing Smoothing (5 times) BeforeAfter
11/29/ Convolve Original Gauss (7x7) ‘Mexican hat’(17x17) Grad N Grad W
11/29/ Nonlinear filters Median (noise eliminate and enhance) Minimum (erode) Maximum (dilate) Open Close
11/29/ Example of morphological (rank) filters Opening (3) Closing (3) Original Minimum, erode (1) Maximum, dilate (1)
11/29/ Example, grain counting Grain imageMaximum (5) Difference
11/29/ Regions and region operation Thresholding, density slicing Erosion, dilation (rank filtering) Skeletons
11/29/ Image analysis Sensitometric Geometric Categorical (image recognition)
11/29/ Segmentation Geometrical shapes Interactive (outlining) Thresholding Filling
11/29/ Segmentation - connected area Density slice, then use wand (auto-outline) to trace outline. Outline written on image with ‘draw boundary’ command.
11/29/ Region of interest (ROI) analysis Area Perimeter Shape Average value Standard deviation
11/29/ Example of measurement AreaMeanLengthMinorMajor
11/29/ Summary Paradigm: scanning, preprocessing, analysis Success depends on all parts of analysis chain Quality control –Quantitative evaluation of performance –Test samples –Repeated analysis
11/29/ 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
11/29/ Houston, we have a problem.