avizo 6 reference guide

Avizo 6Avizo Reference Guide

Copyright Information

c1995-2010 Konrad-Zuse-Zentrum fur Informationstechnik Berlin (ZIB), Germanyc1999-2010 Visualization Sciences Group (VSG) SAS

All rights reserved.

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Avizo Earth and the XLVolume extension include user protection under license for Landmark U.S. Patent Numbers 6,765,570.

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Contents

I Alphabetic Index of Modules 1

1 Avizo 3

1.1 Access LargeDiskData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1.2 AffineRegistration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

1.3 AlignPrincipalAxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7

1.4 AlignSlices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

1.4.1 Tool Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

1.4.2 Menu Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

1.4.3 Alignment Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

1.4.4 Image Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

1.4.5 Key Bindings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

1.5 Animate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

1.6 AnnotatedIsolines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

1.7 Annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

1.8 AnonymizeImageStack . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

1.9 ApplyBSplineTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

1.10 ApplyTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

1.11 ArbitraryCut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

1.12 Arithmetic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

1.13 Axis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

1.14 BoundingBox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

1.15 BumpSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41

1.16 CalculusMatlab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

1.17 CameraPath . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

1.18 CannyEdgeDetector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47

1.19 CastField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

1.20 CastLineSetToSpatialGraph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

1.21 CastSpatialGraphToLineSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

1.22 ChannelWorks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

1.23 CityPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52

1.24 ClippingPlane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

1.25 ClusterDiff . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

1.26 ClusterGrep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

1.27 ClusterSample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

1.28 ClusterStringLabels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

1.29 ClusterView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

1.30 CollectiveTCL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

1.31 ColorCombine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

1.32 Colorwash . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63

1.33 CombineLandmarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

1.34 CompareLatticeData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

1.35 ComputeContours . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

1.36 ComputeVolume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

1.37 ConnectedComponents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

1.38 ContrastControl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

1.39 CorrelationPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

1.40 CreateCluster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75

1.41 Curl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

1.42 CurvedSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

1.43 Cutting Plane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

1.44 CylinderSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

ii CONTENTS

1.45 DataProbe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82

1.46 Delaunay2D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

1.47 DemoMaker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

1.48 DemoSequence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

1.49 DicomSend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

1.50 Digital Image Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

1.51 DisplayColormap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102

1.52 DisplayDate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

1.53 DisplayLogos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

1.54 DisplayTime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

1.55 ExtractSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

1.56 FilteredObliqueSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

1.57 GetCurvature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111

1.58 GridView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

1.59 Grouping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113

1.60 HeightField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

1.61 Histogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

1.62 InterpolateLabels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

1.63 Intersect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119

1.64 Isolines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121

1.65 Isolines (Surface) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

1.66 Isosurface (Regular) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124

1.67 IvDisplay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

1.68 IvToSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

1.69 LabelVoxel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

1.70 LandmarkSurfaceWarp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

1.71 LandmarkView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

1.72 LandmarkWarp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130

1.73 LatticeAccess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

1.74 LegoSurfaceGen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133

CONTENTS iii

1.75 LineProbe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133

1.76 LineSetProbe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

1.77 LineSetView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

1.78 MaterialStatistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

1.79 Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140

1.80 Merge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

1.81 MovieMaker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

1.82 MoviePlayer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

1.82.1 The Avizo Movie Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

1.82.2 Optimized Avizo Movies . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

1.82.3 Which Movie or Image Format Should I Use ? . . . . . . . . . . . . . . . . . 147

1.83 NormalizeImage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150

1.84 ObliqueSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151

1.85 OrthoSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155

1.86 OrthoViewCursor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157

1.87 ParallelMovieMaker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159

1.88 PlotSpreadSheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161

1.89 PointProbe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162

1.90 PointWrap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162

1.91 ProbeToLineSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164

1.92 Projection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164

1.93 ProjectionView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166

1.94 ProjectionViewCursor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168

1.95 RefineTetras . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169

1.96 Relabel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171

1.97 RelabelTetras . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172

1.98 RemeshSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173

1.99 Resample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177

1.99.1 Resampling Non-labeled Data Fields . . . . . . . . . . . . . . . . . . . . . . 177

1.99.2 Resampling Labeled Data Fields . . . . . . . . . . . . . . . . . . . . . . . . 181

iv CONTENTS

1.99.3 Coordinates of the Resampled Data Set . . . . . . . . . . . . . . . . . . . . . 181

1.99.4 Resampling in Progress . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181

1.100 Scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183

1.101 ScanConvertSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184

1.102 SelectLines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185

1.103 SelectRoi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186

1.104 SequenceController . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187

1.105 Shear . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188

1.106 ShowViewerSpreadSheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188

1.107 SmoothSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189

1.108 Sound . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190

1.109 SpatialGraphStats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191

1.110 SpatialGraphView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192

1.111 SplineProbe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

1.112 StandardView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195

1.113 Statistics2D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196

1.114 SurfaceArea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197

1.115 SurfaceCut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198

1.116 SurfaceDistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200

1.117 SurfaceField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202

1.118 SurfaceGen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202

1.119 SurfaceIntersector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204

1.120 SurfacePathView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204

1.121 SurfaceStatistics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206

1.122 SurfaceThickness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206

1.123 SurfaceView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207

1.124 TimeHistoryPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 210

1.125 TimeSeriesControl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211

1.126 Trajectory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212

1.127 TransformAnimation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213

CONTENTS v

1.128 TriangleDistortion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215

1.129 VRML-Export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215

1.130 Vertex Morph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218

1.131 VertexDiff . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219

1.132 VertexShift . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219

1.133 VertexView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220

1.134 ViewerPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223

1.135 VolPro-1000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

1.136 Voltex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230

1.137 VolumeEdit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233

1.138 VolumeEdit2D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235

1.139 VoxelView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235

2 Avizo Earth Edition 239

2.1 2DLine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239

2.2 BoundingBox (seismic) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240

2.3 CroppedVolume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240

2.4 CroppedVolumeAttributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243

2.5 Crossline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244

2.6 Crossline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245

2.7 FaultSticksView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247

2.8 FenceSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248

2.9 FreeSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249

2.10 GlobalLogsSetting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252

2.11 Inline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252

2.12 Inline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254

2.13 Isosurface (seismic) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256

2.14 LogMeasurmentSetting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257

2.15 SeismicAttributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257

2.16 SeismicAxis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258

2.17 SeismicSettings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259

vi CONTENTS

2.18 SeismicSurfaceView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259

2.19 SelectRoi (seismic) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260

2.20 TimeSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263

2.21 TimeSlice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265

2.22 WellData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267

2.23 WellDisplay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268

2.24 WellLog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269

2.25 WellLogDisplay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269

2.26 WellTopDisplay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270

2.27 WellTops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271

2.28 WellTopsSettings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272

2.29 WellsSettings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272

3 Avizo Wind Edition 275

3.1 AnimatedParticles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275

3.2 Arithmetic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277

3.3 BoundaryFlux . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281

3.4 BoundaryView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282

3.5 ComposeVectorField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283

3.6 ConvertToUnstructuredModel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284

3.7 CrossSection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284

3.8 DisplayCriticalPoints3D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286

3.9 DisplayLegend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290

3.10 Force . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291

3.11 GridView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293

3.12 Isosurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294

3.13 LineIntegrals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295

3.14 Magnitude . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297

3.15 Outline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298

3.16 SecondaryVariables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298

3.17 SurfaceIntegrals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307

CONTENTS vii

3.18 SurfaceView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312

3.19 UnstructuredMeshDisplayProperties . . . . . . . . . . . . . . . . . . . . . . . . . . 312

3.20 VectorField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315

3.21 VectorPlane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316

3.22 VolumeIntegrals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319

3.23 VortexCoreline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321

3.24 VorticityIdentification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323

4 Avizo Green Edition 327

4.1 Earth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327

4.2 NetCDFControl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329

5 Avizo XQuant Pack 333

5.1 2DHistogramSegmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333

5.2 ConvertToIM6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341

5.3 Quantification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342

5.4 Quantification-Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349

5.5 Quantification-Threshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350

5.6 WatershedSegmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351

6 Avizo XScreen Pack 353

6.1 CreateVRConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353

6.2 ShowConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357

6.3 VRSettings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360

7 Avizo XLVolume Pack 365

7.1 ArithmeticRendering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365

7.2 CastLattice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366

7.3 ConvertToLargeDiskData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367

7.4 IsosurfaceRendering (LDA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 368

7.5 LDAExpertSettings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369

7.6 ObliqueSlice (LDA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372

viii CONTENTS

7.7 OrthoSlice (LDA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 375

7.8 SEG-Y Wizard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378

7.9 SelectRoi (LDA) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380

7.10 VoltexHighQuality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383

8 Avizo XMesh Pack 389

8.1 AlignSurfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389

8.2 BoundaryConditions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 390

8.3 ComponentField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391

8.4 ComputeTensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 392

8.5 ComputeTensorOutOfCore . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393

8.6 ConePlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395

8.7 ContourView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398

8.8 CreateGradientImage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399

8.9 Displace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 400

8.10 DisplayISL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 400

8.11 Divergence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404

8.12 DuplicateNodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404

8.13 EigenvectorToColor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 405

8.14 ExtractEigenvalues . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406

8.15 FieldCut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 407

8.16 Gradient . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 409

8.17 GridBoundary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 410

8.18 GridCut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 412

8.19 GridToSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 414

8.20 GridVolume (Hexahedra) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 414

8.21 GridVolume (Tetrahedra) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416

8.22 HexToTet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 418

8.23 HexaQuality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419

8.24 IlluminatedLines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 420

8.25 Interpolate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 421

CONTENTS ix

8.26 Isosurface (Hexahedra) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423

8.27 Isosurface (Tetrahedra) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 424

8.28 Lambda2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 426

8.29 LatToHex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 426

8.30 LineStreaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 427

8.31 MagAndPhase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428

8.32 Magnitude . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 428

8.33 ParametricSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429

8.34 ParticlePathlines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 432

8.35 ParticlePlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434

8.36 PlanarISL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437

8.37 PlanarLIC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439

8.38 RateOfStrainTensor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 443

8.39 SeedSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 443

8.40 Splats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 444

8.41 StreamRibbons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 446

8.42 StreamSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 448

8.43 SurfaceISL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 450

8.44 SurfaceLIC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 452

8.45 TensorDisplay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 454

8.46 TetToHex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 456

8.47 TetraCombine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457

8.48 TetraGen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457

8.49 TetraQuality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 459

8.50 TetraVectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461

8.51 TriangleQuality . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 462

8.52 VectorProbe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 463

8.53 Vectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465

8.54 Vectors/Normals (Surface) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466

9 Avizo XMicroscopy Pack 469

x CONTENTS

9.1 BeadExtract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 469

9.2 Convolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 470

9.3 CorrectZDrop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471

9.4 DataPreprocess . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

9.5 Deconvolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473

9.6 DistanceMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475

9.7 FourierTransform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477

9.8 PSFGen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477

10 Avizo XSkeleton Pack 479

10.1 AlignBlocks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 479

10.2 ApplyMask . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 480

10.3 ApplyTemplateToMosaic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481

10.4 AutoSkeleton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 483

10.5 CenterlineTree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 485

10.6 ChamferMap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487

10.7 CheckNetwork . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489

10.8 DisplayMosaic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 490

10.9 DistanceMapSkeleton . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 490

10.10 EvalOnLines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491

10.11 HxScanconvertNeuronTree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 491

10.12 MosaicToLargeDiskData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 492

10.13 RadiusHistogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 494

10.14 SmoothLine . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495

10.15 Thinner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495

10.16 Threshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 497

10.17 TraceLines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 497

11 Avizo XTeam Pack 499

11.1 TeamWork . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 499

12 Avizo XMolecular Pack 501

CONTENTS xi

12.1 AlignMolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501

12.2 AlignSequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 503

12.3 AtomicMolecularDensity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 505

12.4 BondAngleView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 508

12.5 BondCalculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 510

12.6 CompMolInterface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511

12.7 CompMolSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 512

12.8 ComputeHBonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 515

12.9 ComputeSecondaryStructure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 516

12.10 ConfigurationDensity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 517

12.11 CreateSphere . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 520

12.12 HBondView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 521

12.13 MeanMolecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 522

12.14 Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 523

12.15 MolElectrostatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 525

12.16 MolOptimizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527

12.17 MolSurfaceView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 528

12.18 MoleculeLabel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 530

12.19 MoleculeView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 532

12.20 NoncovalentInteractionGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 535

12.21 Observables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536

12.22 PrecomputeAlignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 537

12.23 PseudoElectronDensity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 538

12.24 RankTimeStep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 539

12.25 SecStructureView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541

12.26 TubeView . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 545

II Alphabetic Index of Ports 549

13 Avizo 551

xii CONTENTS

13.1 Port . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551

13.2 Connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554

13.3 MasterConnection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 555

13.4 Port3DPointList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 555

13.5 PortButtonList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 558

13.6 PortButtonMenu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 560

13.7 PortChannelConfig . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 561

13.8 PortColorList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 562

13.9 PortColormap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 563

13.10 PortDoIt . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 565

13.11 PortDrawStyle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 566

13.12 PortFilename . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 566

13.13 PortFloatSlider . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 568

13.14 PortFloatTextN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 570

13.15 PortFontSelection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571

13.16 PortGeneric . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 572

13.17 PortInfo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 574

13.18 PortIntSlider . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575

13.19 PortIntTextN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575

13.20 PortMultiChannel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 576

13.21 PortMultiMenu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 576

13.22 PortRadioBox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 577

13.23 PortSeparator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 578

13.24 PortSharedColormap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579

13.25 PortTabBar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579

13.26 PortText . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 580

13.27 PortTime . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 580

13.28 PortToggleList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 582

CONTENTS xiii

III Alphabetic Index of File Formats 585

14 Avizo 587

14.1 ACR-NEMA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 587

14.2 Amira Script Object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 587

14.3 AmiraMesh Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 587

14.3.1 Fields with Uniform Coordinates . . . . . . . . . . . . . . . . . . . . . . . . 591

14.3.2 Fields with Stacked Coordinates . . . . . . . . . . . . . . . . . . . . . . . . 591

14.3.3 Fields with Rectilinear Coordinates . . . . . . . . . . . . . . . . . . . . . . . 592

14.3.4 Fields with Curvilinear Coordinates . . . . . . . . . . . . . . . . . . . . . . 593

14.3.5 Label Fields for Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . 594

14.3.6 Landmarks for Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . 595

14.3.7 Line Segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 596

14.3.8 Colormaps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 597

14.3.9 Spatial Graph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 598

14.4 AmiraMesh as LargeDiskData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 600

14.5 Analyze 7.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 600

14.6 AnalyzeAVW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601

14.7 Avizo Script . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601

14.8 BMP Image Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601

14.9 DICOM export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 602

14.10 DICOM import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 602

14.11 DXF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608

14.12 Encapsulated PostScript . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608

14.13 HTML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608

14.14 HxSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608

14.15 Icol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 613

14.16 Interfile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 614

14.17 JPEG Image Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 614

14.18 MATLAB Binary Format (.mat) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 614

14.19 MATLAB M-files Format (.m) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 614

xiv CONTENTS

14.20 Nifti . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 615

14.21 Open Inventor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 615

14.22 PNG Image Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 616

14.23 PNM Image Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 616

14.24 PSI format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 616

14.25 Ply Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 618

14.26 Raw Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 618

14.27 Raw Data as LargeDiskData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 620

14.28 SGI-RGB Image Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 620

14.29 STL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 620

14.30 Stacked-Slices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621

14.31 TIFF Image Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 621

14.32 Tecplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623

14.33 VRML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 624

14.34 Vevo Mode Raw Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 625


15.1 CPS-3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 627

15.2 IESX-Card7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 627

15.3 LAS20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 627

15.4 Photon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 628

15.5 SEG-Y . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 628


16.1 Abaqus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 629

16.2 Abaqus Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 629

16.3 Ansys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 630

16.4 Ansys Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 630

16.5 CGNS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 630

16.6 Ensight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631

16.7 FIDAP Neutral . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631

CONTENTS xv

16.8 Fluent/UNS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631

16.9 LSTC LS-Dyna . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 632

16.10 LSTC LS-Dyna Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 632

16.11 Madymo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 632

16.12 Madymo Time-history . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 633

16.13 NASA/Plot3D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 633

16.14 Nastran Bulk Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 633

16.15 Nastran Output2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 633

16.16 Radioss . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 634

16.17 SDRC/IDEAS Universal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 635

16.18 STAR-CCM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 635

16.19 Tecplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 636

17 Avizo Green Edition 637

17.1 NetCDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 637

18 Avizo XScreen Pack 639

18.1 Avizo XScreen Pack Config File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 639


19.1 LDA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 641

19.2 LargeDiskData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 641

19.3 Stacked-Slices as LargeDiskData . . . . . . . . . . . . . . . . . . . . . . . . . . . . 642


20.1 AVS Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 643

20.2 AVS UCD Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 644

20.3 FIDAP NEUTRAL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 644

20.4 Fluent / UNS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 644

20.5 Hypermesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 644

20.6 IDEAS universal format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 645

20.7 Plot 3D Single Structured . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 645

xvi CONTENTS

21 Avizo XMicroscopy Pack 649

21.1 Bio-Rad Confocal Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 649

21.2 FEIStackedScalarField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 649

21.3 FEIUniformScalarField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 649

21.4 Leica 3D TIFF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 649

21.5 Leica Binary Format (.lei) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 650

21.6 Leica Image Format (.lif) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 650

21.7 Leica Slice Series (.info) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 650

21.8 MRC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 650

21.9 Metamorph STK Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 651

21.10 Olympus (.oib/.oif) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 651

21.11 Zeiss LSM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 651


22.1 AMBER . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 653

22.2 AMF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 654

22.3 DX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657

22.4 GROMACS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657

22.5 MAP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658

22.6 MDL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658

22.7 PDB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659

22.8 PHI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661

22.9 PSF/DCD (CHARMM) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661

22.10 Tripos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661

22.11 UniChem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661

22.12 ZIB Molecular File Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 662

23 Avizo XReadCATIA5 Pack 669

23.1 CATIA5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 669

24 Avizo XReadIGES Pack 671

24.1 IGES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 671

CONTENTS xvii

25 Avizo XReadSTEP Pack 673

25.1 STEP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 673

IV Alphabetic Index of Data Types 675

26 Avizo 677

26.1 AnnaScalarField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 677

26.2 AnnaVectorField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 679

26.3 B-Splines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 680

26.4 CameraRotate . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 681

26.5 Cluster . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 681

26.6 ColorField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 683

26.7 Colormap . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 684

26.8 Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 686

26.9 Field3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 687

26.10 HexaGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 688

26.11 HexaScalarField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 689

26.12 IvData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 689

26.13 LandmarkSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 689

26.14 LargeDiskData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 691

26.15 Lattice3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 691

26.16 Light . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 693

26.17 LineSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 695

26.18 Movie . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 697

26.19 MultiChannelField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 699

26.20 Object . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 700

26.21 RawAsExternalData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 702

26.22 RegScalarField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 702

26.23 ScalarField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 702

26.24 ScriptObject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 703

xviii CONTENTS

26.25 SpatialData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 707

26.26 SpatialGraph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 709

26.27 SpreadSheet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 710

26.28 StackedLabelField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 710

26.29 StackedScalarField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 711

26.30 Surface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 712

26.31 Surface Path Set . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 713

26.32 TetraGrid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 714

26.33 TetraScalarField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 715

26.34 Time . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 715

26.35 UniformLabelField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 716

26.36 UniformScalarField3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 717

26.37 VertexSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 718

26.38 ViewBase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 718


27.1 FaultSticks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 723

27.2 FaultSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 723

27.3 Horizon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 723

27.4 MultiVolumeManager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 723

27.5 Seismic2DLineData . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 724

27.6 SeismicVolumeDataObject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 725


28.1 UnstructuredModel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 727

28.2 UnstructuredModelDataSet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 727


29.1 VolumeDataObject . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 729


30.1 AnalyticTensorField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 731

CONTENTS xix

31 Avizo XSkeleton Pack 733

31.1 Mosaic . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 733


32.1 MolSurface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 735

32.2 MolTrajectory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 736

32.3 Molecule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 739

V Alphabetic Index of Editors 751

33 Avizo 753

33.1 Advanced Colormap Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 753

33.1.1 Description of the User-interface Elements . . . . . . . . . . . . . . . . . . . 754

33.1.2 How to Modify a Colormap . . . . . . . . . . . . . . . . . . . . . . . . . . . 758

33.2 CameraPath Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 759

33.3 Color Dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 760

33.4 Colormap Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 763

33.4.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 763

33.4.2 Menu Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 764

33.4.3 Global Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 764

33.4.4 Histogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 765

33.4.5 Gradient Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 765

33.4.6 Alpha Curve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 766

33.4.7 Color Chooser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 767

33.4.8 Opacity Chooser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 767

33.4.9 Control Buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 767

33.5 Curve Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 767

33.6 Data Parameter Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 769

33.7 Datasets Selector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 769

33.8 Demo GUI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 770

33.9 Digital Image Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 774

xx CONTENTS

33.9.1 Noise reduction minimum filter (Minimum) . . . . . . . . . . . . . . . . . . 775

33.9.2 Noise reduction maximum filter (Maximum) . . . . . . . . . . . . . . . . . . 776

33.9.3 Unsharp masking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 776

33.9.4 Laplacian edge detection filter (Laplacian zero-crossing) . . . . . . . . . . . 776

33.9.5 Noise reduction median filter (Median) . . . . . . . . . . . . . . . . . . . . . 776

33.9.6 Gaussian smoothing filter (Gauss) . . . . . . . . . . . . . . . . . . . . . . . 776

33.9.7 Sobel edge detection filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . 777

33.9.8 Equalize filter (Histogram) . . . . . . . . . . . . . . . . . . . . . . . . . . . 777

33.9.9 Edge-Preserving smoothing . . . . . . . . . . . . . . . . . . . . . . . . . . . 777

33.9.10 Resampling/Low pass filter (Lanczos, Phase 0) . . . . . . . . . . . . . . . . . 777

33.9.11 Intensity remapping filter (Sigmoid) . . . . . . . . . . . . . . . . . . . . . . 778

33.9.12 Brightness and contrast filter . . . . . . . . . . . . . . . . . . . . . . . . . . 778

33.9.13 Statistical feature detection filter (Moments) . . . . . . . . . . . . . . . . . . 778

33.9.14 Lighten/Darken filter (Gamma correction) . . . . . . . . . . . . . . . . . . . 779

33.10 ImageCrop Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 779

33.10.1 Cropping an Image by Dragging and Moving the Box . . . . . . . . . . . . . 780

33.10.2 Cropping an Image by Setting Values Explicitly in the Text Fields . . . . . . 780

33.10.3 Adding New Slices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 781

33.10.4 Changing the Size of the Bounding Box . . . . . . . . . . . . . . . . . . . . 781

33.10.5 Flipping Slices in One Dimension . . . . . . . . . . . . . . . . . . . . . . . 781

33.10.6 Exchanging Two Dimensions . . . . . . . . . . . . . . . . . . . . . . . . . . 781

33.11 Landmark Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 781

33.12 LineSet Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 782

33.13 Plot Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 783

33.13.1 Plot Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 784

33.13.2 Editing Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 785

33.13.3 Working with Plot Objects . . . . . . . . . . . . . . . . . . . . . . . . . . . 788

33.13.4 Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 789

33.13.5 Saving Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 789

33.13.6 Saving the Plot State . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 789

CONTENTS xxi

33.13.7 Specific Option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 789

33.14 Segmentation Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 792

33.14.1 Overview of the Segmentation Editor . . . . . . . . . . . . . . . . . . . . . . 792

33.14.2 Manipulating the Material List . . . . . . . . . . . . . . . . . . . . . . . . . 795

33.14.3 Working in 4-viewer Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . 797

33.14.4 Selection Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 798

33.14.5 Segmentation Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 799

33.14.6 Selection Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 802

33.14.7 Label Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 805

33.14.8 Key Bindings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 806

33.15 Simplification Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 808

33.16 Surface Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 810

33.16.1 Menu Entries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 812

33.16.2 Selectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 814

33.16.3 Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 815

33.16.4 Surface boundaries editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . 817

33.17 Surface Path Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 821

33.18 Transform Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 825


34.1 Model Colors Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 827

34.1.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 827

35 Avizo XQuant Pack 829

35.1 IM6 On-disk Calibration Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 829

35.2 Quantification Calibration Unit Editor . . . . . . . . . . . . . . . . . . . . . . . . . . 830


36.1 Grid Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 831


37.1 Molecule Attribute Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 837

xxii CONTENTS

37.2 Molecule Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 844

CONTENTS xxiii

Part I

Alphabetic Index of Modules

Chapter 1

Avizo

1.1 Access LargeDiskData

This module is deprecated. Please use LatticeAccess instead.

This kind of module is attached to a LargeDiskData object. provides an interface to select a subblockof the large volume which is stored on disk only.

You may select the volume either by typing in numbers to the ports or by using the blue dragger in theviewer.

Additionally, it is possible to request a lower resolution of the data. Dependent on the file format otherresolutions are stored on disk and might be accessed rather fast or they are calculated on the fly whichmight take some time.

After selecting a volume you might press the Apply button. An Avizo field object is created and filledwith the data from disk. You can now use all standard Avizo visualization techniques on this subblock.

If you check auto-refresh, you might change the selected volume and an immediate reload is started.This might be useful to easily explore a large volume.

Connections

Data [required]

Connection to the LargeDiskData object.

ROI [optional]

If a SelectRoi is connected it will define the subvolume to be loaded.

Ports

Info

Indicates the size of the block to be loaded.

BoxMin

The position of the lower corner of the block. Printed as a lattice index.

BoxSize

The size of the block to be loaded. The size is in lattice indices in the base resolution. The numberswill not change if you select subsampling but the real size of the block to be loaded will change.This is indicated in the Info port.

Options

Hides the dragger and/or enables subsampling.

Subsample

Type in the number of voxels to be averaged in each dimension.

1.2 AffineRegistrationThis module computes an affine transformation for registration of two image data sets, using an it-erative optimization algorithm. A hierarchical strategy is applied, starting at a coarse resampling ofthe data set, and proceeding to finer resolutions later on. Different similarity measures like Euclideandistance, mutual information, and correlation can be chosen.

To use this module, you must connect it to two scalar fields. To follow the progress visually, a modulelike BoundingBox or Isosurface should be connected to each of them, but this may slow down the reg-istration process. If the Register button of the Action port is pressed, the module starts by successivelyoptimizing the transformation of the first input.

The optimization can be interrupted at any time. Interruption might take some seconds.

Note: In versions of Avizo prior to 4.0, this module was named Registration.

4 Chapter 1: Avizo

ConnectionsModel [required]The model data set to be transformed.

Reference [required]The reference data set to which the model is registered.

Reference2 [optional]See Reference3 below.

Reference3 [optional]The connection ports Reference2 and Reference3 are used for a particular type of images routinelytaken in MRI, so-called Localizers. A Localizer consists of few (3) slices each of an axial/xy,sagittal/yz, and coronal/yz scan. A CT orMR taken from the same patient or object can be registeredto the Localizer images by using high resolution information for each direction in separate volumes.To do so, connect the two additional Reference ports with the Localizer images. Note that the portOptions2: Localizer automatically gets checked.

PortsMetric

This port selects the similarity measure to be applied. Euclidean means the Euclidean distance,i.e. the mean squared difference between the gray values of model and reference. Correlationmeasures the correlation of the registered images. The Mutual information metrics, especially thenormalized one, are recommended when images from different modalities, e.g., CT and MRT, areto be registered.

Transformation

At this port you can select the number of transformation parameters to be optimized. The numbersare 6 for Rigid (3 translations and 3 rotations), 7, 9, and 12 for IsoScale, AnisoScale, and Shear,respectively.

If you select for example Rigid and AnisoScale, on each resolution level the 6 parameters of arigid transformation will be optimized first, followed by an optimization of all 9 parameters of ananisoscale transformation. In this way as much as possible is done using a rigid transformation.

If only AnisoScale is selected, all 9 parameters will be optimized at once. A larger contribution ofthe scaling parameters may be expected for this selection.

Extended options

AffineRegistration 5

If this toggle is unset, only the most important ports are visible. The other ports are set to defaultvalues which should work well in most cases.

If the toggle is selected, the additional ports Optimizer, Optimizer step, QuasiNewton Optimizeron finest N levels, CoarsestResampling, Histogram range reference, Histogram range model, andOptions become visible (see below).

Action

If the Align Centers button is pressed, the centers of gravity of both data sets are computed, takingthe image intensity as a mass density. The model data set is translated in order to align both centersof gravity.

If the Align Principal Axes button is pressed, the centers of gravity and moments of inertia of bothdata sets are computed, again taking the image intensity as a mass density. The principal momentsof inertia and corresponding principal axes are computed. The best of 24 possible alignments of theprincipal axes is determined according to the similarity measure as selected at theMetric port.

Pressing the Register button starts the actual registration process.

Optimizer

At this port you can choose between different optimization strategies. The ExtensiveDirection orBestNeighbor optimizers are well suited for coarse resolution levels, the QuasiNewton or Line-Search optimizers for the finer resolution levels. The default strategy uses the ExtensiveDirectionoptimizer on the coarse levels and the QuasiNewton optimizer on the finest levels.

Optimizer step

This port sets the initial and the final value for the stepwidth to be applied in the optimizations.These stepwidths refer to translations. For rotations, scalings, and shearings appropriate values arechosen accordingly.

The default value for the initial stepwidth is 1/5 of the size of the bounding box. If both data setsare already reasonably aligned, you may choose a smaller initial stepwidth.

The default value for the final stepwidth is 1/6 of the voxel size.

QuasiNewton Optimizer on finest N levels

At this port you can select the number of resolution levels (between 0 and 2) where theQuasiNewtonoptimizer is applied. On the coarser levels the optimizer as selected at port Optimizer is applied.

6 Chapter 1: Avizo

If the number of levels is less than or equal to the number selected at this port, the optimizer asselected at port Optimizer is applied at least at the coarsest level.

CoarsestResampling

At this port you can define the resampling rate for the coarsest resolution level where registrationstarts. The resampling rate refers to the reference data set. If the voxels of the reference data setare anisotropic, i.e. have a different size in x-, y-, and z-direction, the default resampling rates arechosen in order to achieve isotropic voxels on the coarsest level. If the voxel sizes of model andreference differ, the resampling rates for the model are chosen in order to achieve similar voxel sizesas for the reference on the same level.

Histogram range reference

This port is only active if one of the Mutual information metrics has been selected. Here you candefine the range of gray values for the histogram of the reference data set. The essential informationof the data set should be within this range. It is a good idea to determine the range via a visualizationof the data set, e.g., using an OrthoSlice module.

Histogram range model

The same as the previous port, now for the model data set.

Options

If toggle IgnoreFinestLevel is selected, registration will be performed on all but the finest (i.e. theoriginal) resolution. In many cases a sufficient accuracy can be achieved in this way. Registration onthe finest level may slightly improve the accuracy, but the computation time will typically increaseby an order of magnitude.

1.3 AlignPrincipalAxesThis module computes a rigid transformation for a triangulated surface, such that its principal axes arealigned to a reference coordinate system. This can either be the standard basis in 3D or the principalaxes of a reference triangulated surface.

ConnectionsModel [required]Model surface, that will be transformed.

AlignPrincipalAxes 7

Reference [optional]Reference surface, whose principal axes will serve as a reference coordinate system.

PortsOptions

This port is only visible, when a reference surface is connected. For each possible solution (seeexplanation below at Port Action), the root mean square distance is computed, when the optionOptimize distance is chosen. The final transformation will be the one yielding the minimumvalue.

Axis1

If no reference surface is connected, the principal axes with the largest moment of inertia will bealigned to the axis specified at this port.

Axis2

If no reference surface is connected, the principal axes with the second largest moment of inertiawill be aligned to the axis specified at this port.

Action

The Go button starts the alignment. Since the principal axes are only computed up to their orien-tation the model surface can subsequently be rotated 180 degree around each of its principal axesby pressing one of the Rot buttons. The number corresponds the first, second, or third largestmoment respectively.

CommandsgetRefSystem

Prints the center of gravity, the axes of inertia, and the moments of inertia in the console.

1.4 AlignSlicesThis module allows you to interactively align 2D slices of a 3D image stack. Alignment is performedin a separate graphics window that is activated by pressing the Edit button of the modules Action port.To close the slice aligner, press the Close button of the modules Action port.

8 Chapter 1: Avizo

The align window displays by default two consecutive slices using different draw styles that can beselected from the View menu. The two displayed slices can be chosen using the slice slider on the toolbar. Only one of these two slices is editable at a given time. The slice that can be edited is selectableand it can be either the lower or the upper one. By dragging the editable slice using the left mousebutton, the slice will be translated. The slice can be rotated around its center by dragging it whilekeeping the middle mouse button pressed. At any time the numbers of the current slice pair as well asthe quality of the current alignment is displayed in the status bar at the bottom of the align window.The quality value is based on the sum of squared grey-value difference (SSD) between the two slicesbeing aligned. The SSD is computed for all pixels in the area in which the two slices overlap (thesize of this area depends on the transformation of the slices). The SSD is then normed, so that it liesbetween 0 and 1. The quality in alignSlices is 1 minus this value, and therefore also lies between 0(0%/bad) and 1 (100%/best).

The documentation of the align tool is organized into the following sections (click on the links to opena section):

Tool bar - describes the buttons of the tool bar. Menu bar - describes all entries of the menu bar. Image viewer - describes how to align images interactively. Key bindings - provides a list of all hot keys.

1.4.1 Tool Bar

Slice slider:Allows the user to change the slices that are displayed and can be edited. The displayed numberis the number of the editable slice. If this number is n and the editable slice is the upper one,slices n and n-1 are shown. If the editable slice is the lower one, the displayed slices are slices nand n+1.

Zoom in button:Increases the size of the image.

Zoom out button:Decreases the size of the image.

Zoom label:Shows the current zoom factor. E.g., a zoom of 2:1 means that 2 pixels on the screen correspondto one pixel of the original data set (magnification), while 1:4 would mean that four pixels ofthe data set correspond to one pixel on the screen.

Gravity centers button:Sets the gravity centers alignment as the current alignment algorithm.

Least squares button:Sets the least squares alignment as the current alignment algorithm.

AlignSlices 9

Landmarks button:Sets the landmarks alignment as the current alignment algorithm. When this is the active alignmode, the landmarks will be displayed for the current slices. If one of the other two algorithmsis selected, the landmarks are not shown. The selected algorithm is used when the Align currentslices or Align all slices button is pressed or the corresponding menu items are chosen.

Edge detection button:Sets the edge detection alignment as the current alignment algorithm.

Edit landmarks mode:Sets the active edit mode to be editing landmarks. When this is the active edit mode, thelandmarks that have been already defined can be moved/removed and new landmarks can bedefined (see Image Viewer section). This mode can be activated only only when Landmarksbutton is ON (i.e. the active align mode is landmarks alignment).

Edit slice mode:Sets the active edit mode to be editing slices. This means that the editable slice can be trans-lated/rotated.

Lower slice:This button forces the lower slice of the two displayed slices to become editable.

Upper slice:This button forces the upper slice of the two displayed slices to be editable (default).The editable slice can be translated and rotated and landmarks can be defined for it.

Mirror button:A mirroring transformation is applied to the editable slice.

Align current slices:The two currently displayed slices are automatically aligned using the selected algorithm.

Align all slices:All slices of the given 3D data are automatically aligned using the selected algorithm.

1.4.2 Menu Bar

1.4.2.1 View

Zoom In: Increases the magnification factor of the image. Zoom Out: Decreases the magnification factor of the image. Red/Green: If this option is set, the two images are displayed in magenta and green, respec-tively. If both images match perfectly, a gray image is obtained. Color images are first convertedto grayscale and then transformed to magenta and green.

Checkerboard: If this option is set, one image is displayed in the white parts of a checkerboard

10 Chapter 1: Avizo

pattern while the other image is displayed in the black parts. The size of the parts can be adjustedin the Options dialog (see below).

Average: If this option is set the, two images are averaged or blended in the viewer window. Invert: If this option is set, the lower image is inverted. The inverted image is then blended withthe upper image. If both images match perfectly, a constant gray image is obtained. This optionis the default.

Transform parameters: If enabled, an additional toolbar is added which displays the transfor-mation and flip state of the currently editable slice.

XZ view: If enabled, displays a xz view of the data (i.e. aligned on the y axis) and a toolbar forcontrolling the displayed slice number and its zoom factor.

YZ view: If enabled, displays a yz view of the data (i.e. aligned on the x axis) and a toolbar forcontrolling the displayed slice number and its zoom factor.If either or both of these views are enabled, an additional toolbar is displayed. Two text fieldsallow you to specify the min and max Z values of interest. Activate the Auto update toggle forthe orthogonal views to be automatically updated each time you change a slice in the main alignwindow. Press the Update button to request an explicit update.

1.4.2.2 Options

Undo: This menu provides an undo feature that undoes the last operation. Successive invocationof Undo is possible, allowing several operations to be undone. Each operation made manuallyor automatically (translation, rotation, automatic alignment, landmarks editing) can be undone.The maximum number of operations that can be undone is 100.

Redo: This menu provides a redo feature that redoes the last undone operation. Successiveinvocation of Redo is possible after several undo operations.

Reset all: Set the translations on X and Y and the rotation to 0 for all slices. Reset: Set the translations on X and Y and the rotation to 0 for the current slice (the slice that iscurrently editable).

Transform all: This is a toggle option. If the option is ON, the transformations made for theeditable slice are also made for all slices above when the editable slice is the upper one. Thatmeans that the existing alignment of all other slices not involved in the current transformationwill be preserved.

Fix reference: This option decides if a certain slice is used as a reference slice during the entirealignment procedure. The reference slice is marked by a red tag in the Slice slider. The otherslices will be aligned according to this slice.

Read transformation: Reads the AlignTransform and AlignPoints parameters from the inputdata and sets the transformation values accordingly. This is useful to return to a previous savedalignment. This can be seen as another kind of reset or undo.

Save transformation: Save the actual translations, rotations, and landmarks as parameters inthe input data.

AlignSlices 11

1.4.2.3 Align

This menu offers several alignment algorithms that can be selected in order to obtain the best align-ment. The performance of each algorithm is dependent on the data to be aligned. There are fouralignment algorithms that can be chosen:

Gravity centers: Align gravity centers and principal axes Gray values: Least squares algorithm based on gray values Landmarks: Align user-defined sets of landmarks Edge detection: Align the outer bounds of the objects

In addition, this menu allows you to specify which slices to align, as follows:

Align current pair: Align just the current two slices Align all slices: Align all slices

Finally, the Options button of the Align menu opens a tabbed dialog window allowing you to define avariety of alignment-related options. Each tab will be handled separately below. The tabs are: General,Output, View, Edge Detection, and Least Squares.

1.4.2.4 Align/Options/General

Allow rotation in automatic alignment: If this option is checked, rotations are consideredduring the alignment process. By default this option is checked. Translations are always con-sidered.

1.4.2.5 Align/Options/Output

The Output dialog allows the user to give the output images of the image stack a different size thanthe input images. This is especially useful if the slices are rotated or moved during the alignmentprocedure and some areas of single slices are outside the borders of the image stack. Beside this, abackground color for the new areas in the image can be determined. The following image shows thedialog box.

The following parameters can be set using this dialog:

Automatic size: If this feature is activated, a minimal image size is calculated which containsall pixels of all slices. The dimensions and the position of the new bounding box are set suchthat all slices fit in this new bounding box.

Image width: Sets the width of the output image. Image height: Sets the height of the output image. Show borders: Shows the new image borders of the output image in the Slice Aligner.

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Figure 1.1: The Output options window.

AlignSlices 13

Figure 1.2: The Edge detection options window.

Background color: The user can set the background color for the output image. The color canbe set as a gray value or as an RGB color, depending on the type of the input image. The currentbackground color is depicted in the box to the right.

1.4.2.6 Align/Options/View

Size of checkerboard: Adjusts the size of the pattern if view mode is set to checkerboard.

1.4.2.7 Align/Options/Edge Detection

The parameters for the Edge detection algorithm can be set using this dialog:

Matrix dimension: This is the dimension of the matrix which scans the image and decideswhether a pixel belongs to the object or the background.

14 Chapter 1: Avizo

Matrix percentage: This percentage defines the amount of pixels in the surrounding of a pixelwhich have to belong to the object to indicate that this pixel belongs likewise to the object. Theconsidered surrounding is defined by the matrix dimension.

Matrix rastering: This indicates if the surrounding should be rasterized. If so, the alignment isdone in a shorter time.

Image rastering This decides if the image should be downsampled during the alignment pro-cedure. This speeds up the alignment.

Flipping: This option indicates if a possible flipping of the images should be considered. Calculate threshold: This activates an automatic calculation of the threshold. Set threshold: This allows the threshold to be set manually. Background property: This must be set to describe the background of the image. Accordingto this setting, the threshold is interpreted as an upper or a lower boundary of gray values whichseparate the object from the background.

Angle stepsize: This sets the size of the search algorithms angular steps (in degrees). A highervalue speeds up alignment at the cost of accuracy.

1.4.2.8 Align/Options/Least Squares

The following parameters for the gray values algorithm can be set using this dialog:

Max number of iterations: This is only intended to prevent an infinite loop. Step size for translations: The step size used to search for better positions in X and Y. A smallstep size, though in general may lead to more accurate results, also slows down alignment.

Step size for rotations: The step size used for rotations. Scale factor: During the alignment procedure, the image can be downsampled for the firstiterationsteps so that a better result can be reached in a shorter time.

More information about the align methods and the appropriate settings for the methods can be foundin the alignment section.

1.4.3 Alignment Methods

The four different alignment methods are based on different concepts and thus the results may differsignificantly. However, not only the method decides on the result but the right settings for the method.This page shall help to use the best alignment method and to use the right settings. Therefore, thealgorithms behind the methods are briefly described. This requires a little background knowledgeabout mathematics.

Gravity centers: This method calculates a center of gravity of the gray values and the orienta-tion by means of the covariances of the image.

AlignSlices 15

Figure 1.3: The Least squares options window.

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Gray values: This method compares the single gray values of two images. The more pixels oftwo compared slices have the same gray values, the better the alignment will be valued for thismethod. That means that this method tries to move one slice and calculates the difference of thegray values of both images. If the quality is getting higher after the movement, this method willkeep on changing the positions of to slices to each other until a maximum quality according tothe above mentioned feature will be reached.

Landmarks: This method is the one that requires most user interaction. The user can definesome points, so called landmarks, which will be aligned to each other during the process. Themethod is mostly one of the best because the user decides about on the alignment. The problemof this method is that the user has to set all of these landmarks so that this method is verytime-intensive.

Edge detection: This method is an outline-based method. It works in two steps. In the firststep the method tries to identify the object and clears the surrounding of any noise. If the objectis separated

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