1. Chapter 3: CS689 1 Computational Medical Imaging Analysis Chapter 3: Image Representations, Displays, Communications, and Databases Jun Zhang Laboratory for Computational Medical Imaging & Data Analysis Department of Computer Science University of Kentucky Lexington, KY 40506

2. Chapter 3: CS689 2 3.1a: Introduction Biomedical image is a discrete representation in ordered graphical form of a biological object It can be functions of one or two dimensions, generated by a variety of means, sampled within different coordinate systems and dimensions, and having variable quantized magnitude associated with each sample Individual numerical elements in a digital image are pixels (picture elements) for 2D images and voxels (volume picture elements) for 3D images

3. Chapter 3: CS689 3 3.1b: Biomedical Images Biomedical images are generated by a variety of energy transmissions through tissues or cells, (e.g., light, X-ray, magnetic fields, waves) and recorded by a sensor or multiple sensors The mapping relationships between the transmitter, the object, and the sensor(s) are defined physically and mathematically The correspondence between the object and the resulting image can be analytically described and subsequently analysis of the image can be carried out by direct inference, as if the analysis were performed on the object itself

4. Chapter 3: CS689 4 3.2a: Volume Image Representation 3D biomedical images are generally modeled as a “stack of slices” and effectively represented in the computer as a 3D array Important factors in 3D images: organization of the tomographic data, reference coordinate system used to uniquely address its values in three-space, transformations to obtain desired isotropicity and orientation, and useful display of the data, either in “raw” or processed format

5. Chapter 3: CS689 5 3.2b: Volume Image Data Organization Multidimensional biomedical images reconstructed from tomographic imaging systems are characteristically represented as sets of 2D images A pixel contains a value that represents and is related to some local property of the object A pixel has a defined spatial position in two dimensions relative to some coordinate system imposed on the imaged region of interest

6. 3.2 Pixels and an Example Chapter 3: CS689 6

7. 7 3.2c: 3D Voxels 3D images represent the object as adjacent planes through the structure 3D images often contains voxels that are not cubic (the volume is anisotropic), as the thickness of the 2D images is greater than the size of the pixels Many 3D biomedical image processings prior to visualization and analysis involve the creation of isotropic volume images from anisotropic data, using various spatial interpolation methods The third dimension can be time in some cases with 2D images acquired repetitively over some time

8. Chapter 3: CS689 8 3.2d: CT/MRI Image Voxels

9. Chapter 3: CS689 9 3.2e: A Volume Date from 3D Voxels

10. Chapter 3: CS689 10 3.2f: 3D and 4D Images Some 3D representation may consist of spatially correlated 2D images from different scanning modalities, or different scan types within a modality (a multispectral image set) 4D biomedical images are organized as collections of 3D images of varying time 4D organization can also consist of 3D multispectral volume image sets, each represents a different modality or type of acquisition 5D data sets consist of 4D time varying of different modalities

11. Chapter 3: CS689 11 3.3a: Coordinate Systems and Object Orientation The orientation of the structure being imaged is specified in order to standardize the location and orientation of the object in a regular grid, permitting spatial correlation and comparison between volume images One is origin-order system – mathematically rigorous, but not always intuitively obvious The other is view-order consistency – a more natural and intuitive way of conceptualizing 3D volume images, but not mathematically consistent

12. Chapter 3: CS689 12 3.3b: Origin-Order System In origin-order system, the coordinate system maintains an unambiguous, single 3D origin in the volume image with the order of all voxels in a single line of a plane Consistency applied to a left-handed coordinate system, the projection of the origin is always from the origin outward. Volume images can be correctly reformatted into orthogonal sections Flipping images about one or three of the axes corrupts the integrity of the image and results in a volume image that its mirror-reversed

13. Chapter 3: CS689 13 3.3c: View-order Consistency This system is not concerned with the maintenance of a single unambiguous 3D origin. It simply posits a relationship that should hold between the orientation of the sectional images and their order in the data file It accepts sectional images in any of six orientations, and assigns the axes to the row, column, and image directions of the image data regardless of the physical section orientation The main advantage is that it is highly intuitive and completely insensitive to orientation

14. Chapter 3: CS689 14 3.3d: Transverse (Axial) Slices in the XY Plane

15. Chapter 3: CS689 15 3.3e: Sagittal Slices are in the ZY Plane

16. Chapter 3: CS689 16 3.3f: Coronal Slices are in the ZX Plane

17. Chapter 3: CS689 17 3.3g: What is the View of this Slice?

18. Chapter 3: CS689 18 3.3e: What is the View of this Slice?

19. Chapter 3: CS689 19 3.4a: Value Representation At each pixel or voxel, a value is measured and/or computed by the imaging system. The range of the representation must encompass the entire range of possible measured and/or computed values and must be of sufficient accuracy to preserve precision in the measured values This range of representation is the dynamic range of the data, determined by both the imaging system and the numeric scale Discrete representation of value in the computer system cannot capture the entire dynamic range of the acquired signal from the imaging system

20. Chapter 3: CS689 20 3.5a: Interpolation and Transformation Most 3D biomedical volume images are sampled anisotropically, with the slice thickness often significantly greater than the in-plane pixel size Visualization and measurement usually require volume data to be isotropic, and the data must be post-processed before it can be used properly Possible problems for anisotropic data: incorrect aspect ratio along each dimension for visualization, and aliasing artifacts due to difference in sampling frequency

21. Aliasing and Anti-Aliasing Chapter 3: CS689 21

22. Chapter 3: CS689 22 3.5b: Interpolation First-order linear interpolation of the gray level values is commonly used for 3D volume image Values of “new pixels” between existing pixels are simply interpolated (averaged) values of the existing pixels. It is a tri-linear interpolation in 3D. The interpolation in each of the dimensions is completely separable Tri-linear interpolation works well for most biomedical images

23. Chapter 3: CS689 23 3.5b: Linear Interpolation Discrete dataLinear interpolation

24. Chapter 3: CS689 24 3.5b: Polynomial & Spline Interpolation Polynomial interpolationSpline interpolation

25. Chapter 3: CS689 25 3.5c: High Order Interpolation When the ratio in size between any of the voxel dimensions in 3D becomes greater than approximately 5 to 1, tri-linear interpolation does not work well, which will provide poor approximations High order interpolation, such as cubic interpolation, may be used, with increased computational cost Cubic interpolation uses more than the immediate adjacent voxels and uses a cubic polynomial to estimate the intermediate values Shape-based interpolation methods may be used for certain particular (known) structure of interest

26. Chapter 3: CS689 26 3.5c: Nearest Neighbor Interpolation It is fast. Most useful if you need to see directly the voxels of the data you are displaying Thickness of the corornal slices

27. Chapter 3: CS689 27 3.5c: Linear Interpolation Linear between slice interpolation. The data is interpolated with nearest neighbor with the slice plane

28. Chapter 3: CS689 28 3.5c: Tri-Linear Interpolation 3D linear interpolation based on the neighboring voxels to each pixel on the displaced screen slice Blurring of data problem

29. Chapter 3: CS689 29 3.5c: Cubic Interpolation Best quality images Cubic interpolation may take a long time to update on slower machines

30. Chapter 3: CS689 30 3.6a: Computers and Computer Storage In computers, each switch value is referred to as a binary unit, or “bit” 8 bits form a “byte”. A computer word may be of size 8 bits, 16 bits, 32 bits, or 64 bits For evaluation of images by eye, comparative visual sensitivity is limited to approximately 9 bits of gray scale, but the eye can adapt to lighting conditions over about a 20-bit range Radiologists can modify the lighting conditions of the film to take advantage of the entire dynamic range expressed in the film

31. Chapter 3: CS689 31 3.6b: Numeric Values Most computers have “natural” word sizes of 32 or 64 bits, and have special capabilities for handling numeric values of 8 or 16 bits The resolving power of the physical sensors used to capture biomedical images typically does not exceed more than 12 or 14 bits of information Storing 12 bits of data in 32 bits of storage is very inefficient

32. Chapter 3: CS689 32 3.6c: Computer Storage Portable storage media: floppy disk (2MB), digital versatile disk (5,000 MB), flash disk (1GB) Magnetic tapes are ideal for archiving and backing- up computer data Hard disk: high speed and low cost with good reliability, primary devices for operating systems, computer software, and interim data Memory (2GB) and cache (2MB) are faster and temporary storage. They are critical for practical interactive image processing and visualization

33. Chapter 3: CS689 33 3.6d: Storage of Biomedical Images Biomedical images can usually be stored in slow storage media as they are not viewed frequently Design decisions for storage are based on the needs of the practitioners who use images, and balanced against the cost of data storage and software systems needed to make them accessible, reliable, and durable New standards, such as DICOM (Digital Imaging and Communications in Medicine), are evolving that will combine the universal access of film with the flexibility of digital imagery

34. Chapter 3: CS689 34 3.7a: Display Types and Devices The need for 3D display is emphasized by gaining an appreciation of the fundamental dilemma of studying 3D irregularly shaped objects like the organs of the body by using tomographic images 3D displays avoid the necessity of mentally reconstructing a representation of the structure of interest Multidimensional display techniques for 3D tomographic image analysis can be classified into two basic display types based on what is shown to the viewers: direct display and surface display

35. Chapter 3: CS689 35 3.7b: Direct Display Direct display extends the concept of 2D buffer display of tomographic images into three dimensions by presenting the volume image as a 3D distribution of brightness It enables direct visualization of unprocessed image data Examples of 3D displays are holograms and space- filling vibrating mirrors Most direct 3D displays use augmenting equipment, including stereo holograms, stereo viewers, head- mounted display, etc.

36. Chapter 3: CS689 36 3.7b*: Hologram Display Hologram displays with overhead and underneath illumination

37. Chapter 3: CS689 37 3.7c: Stereo Holograms Left Eye Image Red Channel Only Right Eye Image Red Channel Removed Anaglyph Left & Right Images Overlaid

38. Chapter 3: CS689 38 3.7d: Surface Display Surface display is to visualize the surfaces that exist within the image volume (cognition & information) The surface is first identified either manually or in an automated fashion by computer algorithm The identified surface is represented either as a set of contours or as a surface locus within a volume that reflects light from an imaginary light source Surface display shows light reflectors, while direct display show light emitters Direct display facilitates editing and searching

39. Chapter 3: CS689 39 3.7e: Surface Display

40. Shaded Surface Display Chapter 3: CS689 40

41. Chapter 3: CS689 41 3.8a: Color Sensitivity The human visual system is highly sensitive to color. In favorable light, humans can detect more than 1 million colors, and non-color-blind individuals can differentiate 20,000 colors Too many colors in an image usually cause confusion in encoding abstract information X-ray images are usually displayed in black and white. Colors may be added to make the image more vivid (in CT images) Colors may be used to represent maps of functions (temperature, pressure, electrical activity), and to distinguish one anatomical object from its surroundings

42. Chapter 3: CS689 42 3.8b: Colored Brain Images

43. Chapter 3: CS689 43 3.9a: Two-dimensional Displays Modern computer workstations generally include a color “bitmapped” display for visual interaction with the system They generally use cathode ray tubes or large liquid crystal devices (LCD) Bitmapping is a technique of breaking the surface of a 2D display screen into individually addressable pixels The value of each pixel is stored in a memory address in the graphics cards, and is scanned and painted onto the screen by the display system many times per second

44. Chapter 3: CS689 44 3.9b: Presentation Formats For display of biomedical images, the most important characteristics of the display system are the number of bits per pixel, resolution, and color properties 8-bit gray scale or color mapped displays may not be sufficient for some images containing color gradients over large areas For maximum color performance, a graphics display subsystem is implemented with three separate raster channels for each of the red, blue, and green guns in the cathode ray tube. Each color is represented with 8-bit value of pixel

45. Chapter 3: CS689 45 3.9c: Cathode Ray Tube

46. Chapter 3: CS689 46 3.9d: Color Displays on CRT Shadow mask CRT close-upAperture grille CRT close-up

47. Chapter 3: CS689 47 3.10a: Ergonomics (Work Environment) Our ability to statistically distinguish different intensities of light is limited to less than two decades To maximize the use of light-emitting displays, the iris should be fully open The ambient light in the room should be near the dark end of the gray scale of the display system A darkened room is optimum for highly detailed analysis and diagnosis

48. Chapter 3: CS689 48 3.10a: Darkened Room Picture

49. Chapter 3: CS689 49 3.10b: Printing Biomedical Images Printing of digital biomedical images has characteristics similar to image display (pixels per inch and color resolution) Color printing uses color primaries orthogonal to that of display system, since printed materials absorb light whereas displays generate light The colors for printing are cyan, magenta, and yellow. (Red, green, and blue for display) Ink jet printers, laser printers, and dye sublimation printers

50. Chapter 3: CS689 50 3.11a: Three-dimensional Displays Most high performance graphics computers have 3D graphics accelerators – a special hardware to assist in the display of 3D surface images on computer screens These accelerators have clock (processing) speed faster than most CPUs. They construct texture maps and inject them into the rendered scene to paint the surfaces of the graphical objects It is possible to utilize the graphics accelerators to do some numerical computing work, to speed up the computation of image data

51. Chapter 3: CS689 51 3.11b: Stereoscopic Visualization The simplest and most common method of generating 3D image displays is to present a pair of appropriately offset 2D images, one for each eye Cross-fusing is to cross one’s eyes while viewing a pair of images. (Need some practice to adjust the eyes quite rapidly) The picture will fuse into a single perceived image in the center of the two separate images Cross-fused images are popular and effective, but they are not natural vision and can be strenuous

52. Chapter 3: CS689 52 3.11c: 3D Cross-Fusing Stereo View

53. Chapter 3: CS689 53 3.11d: Other 3D Stereo Devices Rapidly alternating the presentation of the two stereoscopic images to the eyes and utilizing the persistence effect in the brain to blend the separate images into a single 3D image Can be produced with computer monitors equipped with double-buffered graphic systems Special glasses are needed to view these alternating images, with an LCD eyepiece that can be switched on and off alternately Need synchronization between the switch and screen

54. Chapter 3: CS689 54 3.11e: 3D Stereo Images

55. Chapter 3: CS689 55 3.12a: DICOM DICOM (Digital Image Communications in Medicine) provides a protocol for transmission of image based on their modality, and incorporates metadata for each image within the message Each DICOM image message provides the basic information required to attach it to a patient or an imaging procedure, encoded information may be redundant DICOM requires the sending and receiving computers to agree on a common basic method of communication, and a set of well-defined services (such as image storage) specified before the message is sent

56. Chapter 3: CS689 56 3.12a: DICOM Demonstration

57. Chapter 3: CS689 57 3.12b: Metadata: The Image Header The first part of many image files provides a description of the image – file header The information in the header is called the metadata (the information about the image) Some file formats use formatted header fields to describe the image, e.g., information can be image type, height and width of the image Flexible fields such as TIFF (tagged image file format) defines a set of tags, or field definitions, that may be present or absent in an image file

58. Chapter 3: CS689 58 3.12c: DICOM File A saved DICOM transmission message file has a type of tagged file format. Everything has a tag, a size, and a value Image pixels are described as the value of a pixel tag There are a minimal set of standard tags required, followed by a minimal set of tags for each modality Many optional tagged values may be included, and the specification includes tags for proprietary data, allowing vendors or developers to encode data specific to their machines or process

59. Chapter 3: CS689 59 3.12c: First Part of a DICOM File

60. Chapter 3: CS689 60 3.12c: A DICOM File, composed with data header and the image

61. Chapter 3: CS689 61 3.12c: Captured DICOM Images

62. Chapter 3: CS689 62 3.12d: Pixel/Voxel Packing Most pixel values are stored as binary numeric values with a fixed number of bits Monochrome data needs a single bit; gray scale data is stored as 8 bits, 12 bits, or 16 bits For images with multiple channels in each pixel, such as color encoded as RGB, image file formats may incorporate packed or planar schemes In packed scheme, pixels are grouped by pixel, such as RGB, RGB, RGB, etc In planar scheme, all of the pixels for one color are placed together as a 2D image, such as RRR, followed by GGG followed by BBB

63. Chapter 3: CS689 63 3.12d: Pixel Packing

64. Chapter 3: CS689 64 3.12e: Image Compression Image compression means to express in compact form the information contained in an image The resulting image should retain the salient (or exact) features necessary for the purpose for which it was captured For legal purpose, it is often necessary to insure that decompression restores the image to the same values by which any diagnosis was based Two main types of image compression algorithms: lossless and lossy

65. Chapter 3: CS689 65 3.12f: Lossless Image Compression Lossless compression perfectly recovers the original image after decompression, and works by simply taking advantage of any redundancy in the image, e.g., Huffman encoding, run-length encoding, etc. Most image data has pixel values or groups of pixels that repeat in a predictable pattern It typically achieves ratios of 2:1 or 3:1 on medical images

66. Chapter 3: CS689 66 3.12f: Lossless Compression

67. Chapter 3: CS689 67 3.12g: Run-length Encoding The image pixels are scanned by rows, and a count of successive pixel values along with one copy of the pixel are sent to the output Very effective for large area of constant color Not good for images containing many smooth gradations of gray or color values An example: Original 2211333334333222 (16 characters) Compressed 22 21 53 14 33 32 (12 characters)

68. Chapter 3: CS689 68 3.12g: Run-Length Encoding

69. Chapter 3: CS689 69 3.12g: Run-Length Encoding

70. Chapter 3: CS689 70 3.12g: Run-Length Encoding

71. Chapter 3: CS689 71 3.12h: Huffman and Limpel-Ziv Coding These schemes search for patterns in the data that can be represented by a smaller number of bits These patterns are mapped to a number of representative bytes and stored by probabilities Original 12334123343212334 (17 characters) Map 12334 = A, 32 = B Compressed AABA (13 characters)

72. Chapter 3: CS689 72 3.12i: Lossy Image Compression Lossy compression changes the image values, but attempts to do so in a way that is difficult to detect or has negligible effect on the purpose for which the image will be used It can accomplish 10:1 to 80:1 compression ratios before change in the image is detectable or deleterious Typical techniques are JPEG and wavelets Most often used to reduce bandwidth required to transmit image data over internet

73. Chapter 3: CS689 73 3.12i: Lossy Compression

74. Chapter 3: CS689 74 3.12j: JPEG The JPEG standard was developed for still images, and performs best on photographs of real-world scenes The first pass transforms the color space of the image to a luminance-dominated color space, and then downsamples the image and partitions it into selected blocks of pixels A discrete cosine transform (DCT) is applied to the blocks The resulting DCT values for each block are divided by a quantization coefficients and rounded to integers The reduced data is encoded using Huffman etc

75. Chapter 3: CS689 75 3.12j*: JPEG Lossy Compression Original: 43KMedium compress: 13K Too much: 3.5k 256 colors in Netscape

76. Chapter 3: CS689 76 3.12l: Wavelets Wavelet transform coefficients are partially localized in both space and frequency, and form a multiscale representation of the image with a constant scale factor, leading to localized frequency subbands with equal widths on a logarithmic scale Wavelet compression exploits the fact that real- world images tend to have internal morphological consistency, locally luminance values, oriented edge continuations, and higher order correlations, like textures For CT images, the compression ratio can be 80:1 For chest X-rays, the ratio may be around 10:1

77. Chapter 3: CS689 77 3.12l*: Example of Wavelet Compression Original image 589824 bytes JPEG image 45853 bytes Wavelet image 45621 bytes

78. Chapter 3: CS689 78 3.12l: Wavelet Compression

79. Chapter 3: CS689 79 3.13a: Image Database Basic requirements for an image database are a means to efficiently store and retrieve the images using an indexing method Hierarchical file systems, combine hard disk drives with optical or magnetic tape media, and through a file system database provide what appears to be a monolithic set of files to the users Frequent requests for a large number of files may swamp such a system

80. Chapter 3: CS689 80 3.13b: Where to Store the Images The images can be stored “inside” or “outside” of the databases A much smaller metadata about the image can be stored in the database A small-scale reference image, called “thumbnail”, extracted from the image can be used in a metadata. It is several orders of magnitude smaller than the original image An index is needed to link the metadata with the original image

81. Chapter 3: CS689 81 3.13b: Thumbnail Example

82. Chapter 3: CS689 82 3.13c: DICOM Database DICOM database provides a hierarchical tree structure wherein the patient is at the top of the tree For each patient, there can be several studies, including an image examination by a given modality Within each study, there can be a series of images, where each series can represent different viewpoints of the patient within the study Each series may be a single or a set of images DICOM inherently organizes images in a most suitable way for use in a treatment setting

83. Chapter 3: CS689 83 3.13d: DICOM Data Hierarchy

84. Chapter 3: CS689 84 3.13e: DICOM Database (I)

85. Chapter 3: CS689 85 3.13f: DICOM Database (II)

86. Chapter 3: CS689 86 3.13f: DICOM Database (III)