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xvii | |
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xxiii | |
Foreword |
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xxv | |
Preface |
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xxvii | |
Introduction |
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xxxi | |
About the Authors |
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xxxiii | |
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List of Symbols and Abbreviations |
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xxxv | |
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I Introduction to Images and Computing using Python |
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1 | (54) |
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3 | (20) |
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3 | (1) |
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4 | (1) |
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5 | (3) |
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6 | (1) |
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1.3.2 Enthought Python Distribution (EPD) |
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6 | (1) |
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7 | (1) |
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1.4 Running a Python Program |
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8 | (1) |
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1.5 Basic Python Statements and Data Types |
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8 | (11) |
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11 | (8) |
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19 | (1) |
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20 | (3) |
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2 Computing using Python Modules |
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23 | (14) |
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23 | (1) |
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23 | (3) |
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24 | (1) |
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24 | (2) |
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26 | (5) |
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2.3.1 Numpy Array or Matrices? |
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30 | (1) |
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31 | (1) |
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32 | (1) |
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2.6 Python Imaging Library |
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33 | (1) |
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33 | (1) |
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34 | (1) |
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34 | (1) |
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35 | (2) |
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3 Image and its Properties |
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37 | (18) |
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37 | (1) |
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3.2 Image and its Properties |
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38 | (6) |
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38 | (1) |
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39 | (2) |
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41 | (1) |
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42 | (1) |
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3.2.5 Connectivity: 4 or 8 Pixels |
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43 | (1) |
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44 | (5) |
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44 | (1) |
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44 | (1) |
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45 | (4) |
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3.4 Data Structures for Image Analysis |
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49 | (2) |
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49 | (1) |
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50 | (1) |
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50 | (1) |
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51 | (2) |
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53 | (1) |
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53 | (2) |
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II Image Processing using Python |
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55 | (152) |
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57 | (32) |
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57 | (1) |
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58 | (11) |
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60 | (4) |
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64 | (2) |
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66 | (2) |
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68 | (1) |
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4.3 Edge Detection using Derivatives |
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69 | (16) |
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4.3.1 First Derivative Filters |
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71 | (8) |
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4.3.2 Second Derivative Filters |
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79 | (6) |
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85 | (1) |
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86 | (3) |
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89 | (20) |
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89 | (1) |
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89 | (2) |
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91 | (1) |
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5.4 Power Law Transformation |
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92 | (5) |
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97 | (2) |
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5.6 Histogram Equalization |
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99 | (4) |
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103 | (3) |
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106 | (1) |
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107 | (2) |
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109 | (30) |
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109 | (1) |
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6.2 Definition of Fourier Transform |
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110 | (3) |
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6.3 Two-Dimensional Fourier Transform |
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113 | (5) |
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6.3.1 Fast Fourier Transform using Python |
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115 | (3) |
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118 | (2) |
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6.4.1 Convolution in Fourier Space |
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119 | (1) |
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6.5 Filtering in Frequency Domain |
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120 | (17) |
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6.5.1 Ideal Lowpass Filter |
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120 | (3) |
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6.5.2 Butterworth Lowpass Filter |
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123 | (2) |
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6.5.3 Gaussian Lowpass Filter |
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125 | (2) |
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6.5.4 Ideal Highpass Filter |
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127 | (3) |
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6.5.5 Butterworth Highpass Filter |
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130 | (2) |
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6.5.6 Gaussian Highpass Filter |
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132 | (2) |
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134 | (3) |
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137 | (1) |
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138 | (1) |
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139 | (26) |
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139 | (1) |
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7.2 Histogram Based Segmentation |
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139 | (12) |
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141 | (3) |
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144 | (5) |
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7.2.3 Adaptive Thresholding |
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149 | (2) |
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7.3 Region Based Segmentation |
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151 | (10) |
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7.3.1 Watershed Segmentation |
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153 | (8) |
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7.4 Segmentation Algorithm for Various Modalities |
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161 | (1) |
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7.4.1 Segmentation of Computed Tomography Image |
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161 | (1) |
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7.4.2 Segmentation of MRI Image |
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161 | (1) |
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7.4.3 Segmentation of Optical and Electron Microscope Image |
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162 | (1) |
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162 | (1) |
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163 | (2) |
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8 Morphological Operations |
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165 | (24) |
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165 | (1) |
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165 | (1) |
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166 | (5) |
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171 | (4) |
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8.5 Grayscale Dilation and Erosion |
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175 | (1) |
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176 | (3) |
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179 | (5) |
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8.8 Thickening and Thinning |
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184 | (2) |
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185 | (1) |
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186 | (1) |
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187 | (2) |
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189 | (18) |
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189 | (1) |
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189 | (5) |
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194 | (7) |
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194 | (3) |
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197 | (4) |
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201 | (4) |
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205 | (1) |
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205 | (2) |
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207 | (106) |
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10 X-Ray and Computed Tomography |
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209 | (38) |
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209 | (1) |
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209 | (1) |
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210 | (6) |
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10.3.1 X-Ray Tube Construction |
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210 | (2) |
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10.3.2 X-Ray Generation Process |
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212 | (4) |
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216 | (3) |
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216 | (2) |
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10.4.2 Lambert Beer Law for Multiple Materials |
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218 | (1) |
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219 | (5) |
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220 | (1) |
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221 | (2) |
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10.5.3 Flat Panel Detector (FPD) |
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223 | (1) |
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224 | (2) |
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224 | (1) |
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224 | (2) |
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10.7 Computed Tomography (CT) |
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226 | (10) |
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227 | (1) |
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227 | (1) |
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10.7.3 Central Slice Theorem |
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228 | (4) |
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232 | (1) |
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233 | (1) |
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234 | (2) |
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10.8 Hounsfield Unit (HU) |
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236 | (1) |
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237 | (6) |
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10.9.1 Geometric Misalignment Artifacts |
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238 | (1) |
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238 | (2) |
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10.9.3 Offset and Gain Correction |
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240 | (1) |
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241 | (1) |
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242 | (1) |
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243 | (1) |
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244 | (3) |
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11 Magnetic Resonance Imaging |
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247 | (28) |
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247 | (1) |
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11.2 Laws Governing NMR and MRI |
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248 | (3) |
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248 | (1) |
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249 | (1) |
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250 | (1) |
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251 | (4) |
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11.3.1 Gyromagnetic Ratio |
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251 | (1) |
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252 | (1) |
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11.3.3 T1 and T2 Relaxation Times |
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253 | (2) |
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11.4 NMR Signal Detection |
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255 | (1) |
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11.5 MRI Signal Detection or MRI Imaging |
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256 | (3) |
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258 | (1) |
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258 | (1) |
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11.5.3 Frequency Encoding |
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259 | (1) |
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259 | (4) |
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259 | (1) |
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260 | (1) |
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261 | (1) |
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262 | (1) |
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11.7 T1, T2 and Proton Density Image |
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263 | (2) |
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11.8 MRI Modes or Pulse Sequence |
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265 | (3) |
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265 | (1) |
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11.8.2 Inversion Recovery |
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266 | (1) |
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11.8.3 Gradient Echo Imaging |
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267 | (1) |
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268 | (4) |
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269 | (2) |
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271 | (1) |
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11.9.3 Inhomogeneity Artifact |
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271 | (1) |
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11.9.4 Partial Volume Artifact |
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272 | (1) |
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272 | (1) |
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273 | (2) |
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275 | (20) |
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275 | (1) |
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276 | (6) |
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276 | (1) |
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12.2.2 Numerical Aperture |
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277 | (1) |
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278 | (2) |
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280 | (1) |
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12.2.5 Point Spread Function (PSF) |
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281 | (1) |
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12.2.6 Wide-Field Microscopes |
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282 | (1) |
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12.3 Construction of a Wide-Field Microscope |
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282 | (2) |
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284 | (1) |
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12.5 Fluorescence Microscope |
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284 | (4) |
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284 | (1) |
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12.5.2 Properties of Fluorochromes |
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285 | (2) |
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287 | (1) |
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12.6 Confocal Microscopes |
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288 | (1) |
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12.7 Nipkow Disk Microscopes |
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289 | (2) |
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12.8 Confocal or Wide-Field? |
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291 | (1) |
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292 | (1) |
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293 | (2) |
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295 | (18) |
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295 | (1) |
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296 | (5) |
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297 | (1) |
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13.2.2 Interaction of Electron with Matter |
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298 | (1) |
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13.2.3 Interaction of Electrons in TEM |
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299 | (1) |
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13.2.4 Interaction of Electrons in SEM |
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300 | (1) |
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301 | (5) |
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301 | (2) |
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13.3.2 Electromagnetic Lens |
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303 | (1) |
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304 | (2) |
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13.4 Specimen Preparations |
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306 | (1) |
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307 | (1) |
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308 | (1) |
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309 | (2) |
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311 | (2) |
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A Installing Python Distributions |
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313 | (10) |
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313 | (5) |
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313 | (3) |
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A.1.2 Enthought Python Distribution |
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316 | (1) |
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A.1.3 Updating or Installing New Modules |
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316 | (2) |
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318 | (5) |
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A.2.1 Enthought Python Distribution |
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318 | (1) |
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A.2.2 Installing New Modules |
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318 | (5) |
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B Parallel Programming Using MPI4Py |
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323 | (10) |
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323 | (1) |
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B.2 Need for MPI in Python Image Processing |
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324 | (1) |
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B.3 Introduction to MPI4Py |
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325 | (1) |
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326 | (1) |
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327 | (4) |
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B.5.1 Point-to-Point Communication |
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327 | (2) |
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B.5.2 Collective Communication |
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329 | (2) |
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B.6 Calculating the Value of PI |
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331 | (2) |
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333 | (4) |
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333 | (1) |
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334 | (3) |
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D MATLAB® and Numpy Functions |
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337 | (4) |
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337 | (4) |
Bibliography |
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341 | (10) |
Index |
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351 | |