《植物生理学》课程教学资源：课程参考资料：常用仪器操作方法（PDF电子版）图像处理方法Image J User Guide（IJ 1.46r, Revised edition）

ImageJ s User Guide IMAGEJ/FIJI 1.46 TOgO

ImageJ User Guide ImageJ User Guide Revised edition IJ 1.46r ImageJ/Fiji 1.46

ontents Release Notes for ImageJ 1. 46r Noteworthy Macro Listings Conventions I Getting Started 1 Introduction 2 Installing and Maintaining ImageJ 2.1 Image Distributions 2.2 Related software 2.3 Image 2 3 Getting Help 12235556 3.1 Help on Image Analys 3.2 Help on ImageJ II Working with ImageJ 4 Using Keyboard Shortcuts 5 Finding command 889 6 Undo and redo 7 Image Types and Format 8 Stacks, Virtual Stacks and Hyperstacks 2 9 Color Images 10 Selections 10.1 Manipulating ROIs 18 10.2 Composite Selections 10.3 Selections With Sub-pixel Coordinate 11 Overlays 9 1 2 3D Volumes 1 3 Settings and preferences III Extending ImageJ 14 Macros

Contents Release Notes for ImageJ 1.46r vii Noteworthy viii Macro Listings ix Conventions x I Getting Started 1 Introduction 1 2 Installing and Maintaining ImageJ 2 2.1 ImageJDistributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2.2 Related Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 2.3 ImageJ2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 3 Getting Help 5 3.1 Help on Image Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 3.2 Help on ImageJ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 II Working with ImageJ 4 Using Keyboard Shortcuts 8 5 Finding Commands 8 6 Undo and Redo 9 7 Image Types and Formats 10 8 Stacks, Virtual Stacks and Hyperstacks 12 9 Color Images 14 10 Selections 17 10.1 Manipulating ROIs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 10.2 Composite Selections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 10.3 Selections With Sub-pixel Coordinates . . . . . . . . . . . . . . . . . . . . . . . 19 11 Overlays 19 12 3D Volumes 21 13 Settings and Preferences 22 III Extending ImageJ 14 Macros 23 ii

15 Scripts 16 Plugins 17 Scripting in Other Languages 18 Running ImageJ From the Command Line IV ImageJ User Interface 1 9 Tools 19.1 Area Selection Tool ction tools 19.3 Arrow Tool 19.4 Angle Tool 19.5 Point Tool 19.6 Multi-point Tool 19.7 Wand Tool 19. 8 Text Tool 19.9 Magnifying G 19.10 Scrolling Tool 36 19.11 Color Picker Tool 19.12 More Tools Menu 19.13 Arrow 19.14 Brush 19.15 Developer Menu 19.16 Flood Filler 19.17 LUT Menu 19 18 Overlay Brush 19.19 Pencil 19.20 Pixel Inspector 19.21 Spray Can 19 22 Stacks Menu 20 Custom Tools 41 21 Contextual menu 22 Results table 23 Editor 44 24 Log Window 25 Customizing the ImageJ Interface 25.1 Floating Behavior of Main Window 5.2 Pointer 47 v Menu command 26 FileD 26.1 NewN

15 Scripts 24 16 Plugins 24 17 Scripting in Other Languages 26 18 Running ImageJ From the Command Line 26 IV ImageJ User Interface 19 Tools 19.1 Area Selection Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 19.2 Line Selection Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 19.3 Arrow Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 19.4 Angle Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 19.5 Point Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 19.6 Multi-point Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 19.7 Wand Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34 19.8 Text Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 19.9 Magnifying Glass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 19.10 Scrolling Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 19.11 Color Picker Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 19.12 More Tools Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 19.13 Arrow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 19.14 Brush . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 19.15 Developer Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 19.16 Flood Filler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 19.17 LUT Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 19.18 Overlay Brush . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 19.19 Pencil . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 19.20 Pixel Inspector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 19.21 Spray Can . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 19.22 Stacks Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 20 Custom Tools 41 21 Contextual Menu 42 22 Results Table 43 23 Editor 44 24 Log Window 46 25 Customizing the ImageJ Interface 46 25.1 Floating Behavior of Main Window . . . . . . . . . . . . . . . . . . . . . . . . . 46 25.2 Pointer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 V Menu Commands 26 File . 49 26.1 New. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 iii

26.2 Open.o pen Next OI 26.4 Open Samples 26.5 Open Recent 51 26.6 Import 26.7 Close [w 26.8 Close Al 26.9 Save [ s 26.10 Save AsD 26.11 Revert [r] 26 12 Page Setup 26.13 Print..P 26 14 Quit 27 Edit 271Undo团2] 272cut冈] 27.3 Copy c 27.4 Copy to System 61 27.5 Paste v 27.6 Paste Control 27.7Cl 27.8 Clear Outside 279F 27.10Draw向d 27.11 Invert [ 27.12 Selection D 27.13 Optionsb 28 ImageD 28.1 Type 75 28.2 AdjustS 28.3 Show Info.[ 28.4 Pre 28.5 Colorb 28.6 Stacks> 28.7 Hyperstacksb 28.8Crop凶 97 28.9 Duplicate.. DI 8.10 Rename 28.11 Scale.. EI 98 28.12 Transforms 28.13 Zoom D 28.14 Overlay D 28.15 Lookup Tables 105 29 ProcessD 29.1 Smooth S arden 107 29.3 Find Edges 107 29.4 Find Maxima 107 29.5 Enhance Contrast

26.2 Open. . . [o] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 26.3 Open Next [O] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 26.4 Open Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 26.5 Open Recent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 26.6 Import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 26.7 Close [w] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 26.8 Close All . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 26.9 Save [s] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 26.10 Save As . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 26.11 Revert [r] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 26.12 Page Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 26.13 Print. . . [p] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 26.14 Quit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 27 Edit . 61 27.1 Undo [z] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 27.2 Cut [x] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 27.3 Copy [c] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 27.4 Copy to System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 27.5 Paste [v] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 27.6 Paste Control. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 27.7 Clear . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 27.8 Clear Outside . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 27.9 Fill [f] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 27.10 Draw [d] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 27.11 Invert [I] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 27.12 Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 27.13 Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68 28 Image . 75 28.1 Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 28.2 Adjust . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 28.3 Show Info. . . [i] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82 28.4 Properties. . . [P] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 28.5 Color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 28.6 Stacks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 28.7 Hyperstacks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96 28.8 Crop [X] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 28.9 Duplicate. . . [D] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97 28.10 Rename. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 28.11 Scale. . . [E] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 28.12 Transform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98 28.13 Zoom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 28.14 Overlay . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 28.15 Lookup Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 29 Process . 107 29.1 Smooth [S] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 29.2 Sharpen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 29.3 Find Edges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 29.4 Find Maxima. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 29.5 Enhance Contrast. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 iv

29.6 NoiseD 110 9.7 Shadows 29.8 Binary b 112 29.9 Math 9.10 FFTD 29.11 Filters 124 9.12 Batch 29. 13 Image Calculator 128 9.14 Subtract Background 29. 15 Repeat Command [R] 30 AnalyzeD 132 30.1 Measure..m 132 30.2 Analyze Particles 132 30.3 Summarize 30.4 Distribution 135 30.5 Label 136 30.6 Clear results 30.7 Set Measurements 30.8 Set Scale 30.9 Calibrate 30.10 Histogram [h] 30.11 Plot Profile [k] 142 30.12 Surface Plot 30 13 Gels 144 30.14 Tools 146 31 Plugins 156 B11 Macros 31.2 Shortcuts 31.3 Utilities 158 31.4 Newp 161 31.5 Compile and Run 32.1 Show All[I 163 32.2 Put Behind [tab 32.3 Cascade 32.4 Tile 33 HeloD 164 33.1 ImageJ Website 164 33.2 Imagej News 164 33.3 Documentation 164 33.4 Installation 33.5 Mailing Lis 164 33.6 Dey. resources 164 33.7 Plugins 164 33.8 Macros 164 33.9 Macro Functions 33.10 Update ImageJ 165 33.11 Refresh Menus

29.6 Noise . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110 29.7 Shadows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111 29.8 Binary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112 29.9 Math . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117 29.10 FFT. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 29.11 Filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124 29.12 Batch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 29.13 Image Calculator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128 29.14 Subtract Background. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129 29.15 Repeat Command [R] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131 30 Analyze . 132 30.1 Measure. . . [m] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 30.2 Analyze Particles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132 30.3 Summarize . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 30.4 Distribution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 30.5 Label . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136 30.6 Clear Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136 30.7 Set Measurements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 136 30.8 Set Scale. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 30.9 Calibrate. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 30.10 Histogram [h] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140 30.11 Plot Profile [k] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142 30.12 Surface Plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 30.13 Gels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 30.14 Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146 31 Plugins . 156 31.1 Macros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156 31.2 Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 31.3 Utilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158 31.4 New. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 31.5 Compile and Run. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162 32 Window . 163 32.1 Show All [ ] ] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 32.2 Put Behind [tab] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 32.3 Cascade . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 32.4 Tile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 33 Help . 164 33.1 ImageJ Website. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 33.2 ImageJ News. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 33.3 Documentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 33.4 Installation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 33.5 Mailing List. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 33.6 Dev. Resources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 33.7 Plugins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 33.8 Macros. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 33.9 Macro Functions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164 33.10 Update ImageJ. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 33.11 Refresh Menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 v

33 12 About Plugins 165 33. 13 About ImageJ 165 VI Keyboard Shortcuts 4 Key Modifiers 34.1 Alt Key modifications 167 34.2 Shift Key Modifications 34.3 Ctrl (or Cmd) Key Modifications 34.4 Space Bar 169 34.5 Arrow Keys 35 Toolbar shortcuts Credits 171 ImageJ Related Publications 174 List of abbreviations and ac 181 Index 182 Colophon 186

33.12 About Plugins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 33.13 About ImageJ. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165 VI Keyboard Shortcuts 34 Key Modifiers 34.1 Alt Key Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 34.2 Shift Key Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168 34.3 Ctrl (or Cmd) Key Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . 169 34.4 Space Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 34.5 Arrow Keys . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 35 Toolbar Shortcuts Credits 171 ImageJ Related Publications 174 List of Abbreviations and Acronyms 181 Index 182 Colophon 186 vi

Summarized release notes for lmage 1, 46r Selections with sub-pixel resolution Improved handling of Overlays Fourtneen new macro functions New tools: Arrow, Brush, Developer Menu, Flood Filler, LUT Menu, Overlay Brush Pencil, Pixel Inspector, Spray Can and Stacks Menu Customizable crosshair cursor Improved AvI New command: File b Import b XY Coordinates Undo support extended to Edit b Selection b command New command: Edit b Selection b Interpolate Edit b Selection b Line to Area now works with one pixel wide straight lines New command: Edit D Selection b Image to Selection New command: Edit b Options b Reset Image b Color b Merge Channels.. extended to 7 channels Color Choosers display hex color values Improved Image Stacks b Tools b Concatenate New command: Image b Transform b Bin New commands: Imageb Transform b Image to Results and Results to Image 100 New command: Image b Overlay b Labels 104 New command: Image b Overlay b Overlay Options 105 New command: Editb Selection b Gaussian Blur 3D Live histograms 140 Live profile plots 142 Much improved Curve Fitter 148 The ROI Manager now uses an overlay to display selections when in Show All mode New command: ROI Manager's Print List 152 New command: Analyze b Tools b Synchronize Windows New commands: Plugins D New b Macro/Plugin Tool 161 Please note that this is not an extensive list. Detailed release notes for version 1. 46r are available on the ImageJ newswebsitehttp://imagej.nihgov/ij/notes.html

*Summarized Release Notes for ImageJ 1.46r Selections with sub-pixel resolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Improved handling of Overlays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 Fourtneen new macro functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24 New tools: Arrow, Brush, Developer Menu, Flood Filler, LUT Menu, Overlay Brush, Pencil, Pixel Inspector, Spray Can and Stacks Menu . . . . . . . . . . . . . . . . . . 38 Plugin Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 Customizable crosshair cursor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47 Improved AVI support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 New command: File . Import . XY Coordinates. . . . . . . . . . . . . . . . . . . . . . . . . . . 55 Undo support extended to Edit . Selection . commands . . . . . . . . . . . . . . . . . . . . 63 New command: Edit . Selection . Interpolate . . . . . . . . . . . . . . . . . . . . . . . . . . 64 Edit . Selection . Line to Area now works with one pixel wide straight lines . . . . . . . . . 66 New command: Edit . Selection . Image to Selection. . . . . . . . . . . . . . . . . . . . . . . . 67 New command: Edit . Options . Reset. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74 Image . Color . Merge Channels. . . extended to 7 channels . . . . . . . . . . . . . . . . . . . 83 ColorChoosers display hex color values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 Improved Image . Stacks .Tools . Concatenate. . . . . . . . . . . . . . . . . . . . . . . . . . . 93 New command: Image .Transform . Bin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 New commands: Image .Transform . Image to Results and Results to Image . . . . . . . . . 100 New command: Image . Overlay . Labels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 New command: Image . Overlay . Overlay Options. . . . . . . . . . . . . . . . . . . . . . . . . 105 New command: Edit . Selection . Gaussian Blur 3D. . . . . . . . . . . . . . . . . . . . . . . . 125 Live histograms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140 Live profile plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142 Much improved Curve Fitter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148 The ROI Manager now uses an overlay to display selections when in Show All mode . . . 151 New command: ROI Manager’s Print List . . . . . . . . . . . . . . . . . . . . . . . . . . . 152 New command: Analyze .Tools . Synchronize Windows . . . . . . . . . . . . . . . . . . . . . 154 New commands: Plugins .New. Macro/Plugin Tool . . . . . . . . . . . . . . . . . . . . . . 161 Please note that this is not an extensive list. Detailed release notes for version 1.46r are available on the ImageJ news web site: http://imagej.nih.gov/ij/notes.html. vii

Noteworthy Frontmost window and window activation II Image Types: Lossy Compression and Metadata III Opening Virtual Stacks by Drag Drop 13 Iv Replacing Red with Magenta in RGB Images v Toggling calibrated Units VI Opening File Paths in the Log window VII Organizing Commands in the Menu Bar VIII Opening Files: FileD Open., Fileb Import b and Drag Drop IX Reducing Memory Requirements When Importing Images Warning on JPEG Compression XI Drawing Lines wider Than One-Pixel KII Transferring Selections Between Images XIlI Converting Composite Selections XIV Applying Auto Brightness/Contrast to Entire Stacks Xv Display Range of DICOM Images XVI Brightness /Contrast of High Bit-Depth Images XVIl Embedding Color Annotations in Grayscale Images XVIll Working with Zoomed Canvases XIX Hexadecimal color values XX Creating Binary Masks 113 XXI Skeletonize vs skeletonize 3D 115 KXII Interpreting Binary Images 118 XXIII Global Calibrations 141 XXIV Using Scanners in Densitometry 144 XXV Selecting ROIs in the ROI Manager 153 XXVI Focus on bioimage informatics 173

Noteworthy I Frontmost Window and Window Activation . . . . . . . . . . . . . . . . . . . . . 9 II Image Types: Lossy Compression and Metadata . . . . . . . . . . . . . . . . . . . 12 III Opening Virtual Stacks by Drag & Drop . . . . . . . . . . . . . . . . . . . . . . . 13 IV Replacing Red with Magenta in RGB Images . . . . . . . . . . . . . . . . . . . . 16 V Toggling Calibrated Units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 VI Opening File Paths in the Log Window . . . . . . . . . . . . . . . . . . . . . . . 46 VII Organizing Commands in the Menu Bar . . . . . . . . . . . . . . . . . . . . . . . 48 VIII Opening Files: File . Open. . . , File . Import . and Drag & Drop . . . . . . . . . . . 50 IX Reducing Memory Requirements When Importing Images . . . . . . . . . . . . . 53 X Warning on JPEG Compression . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 XI Drawing Lines Wider Than One–Pixel . . . . . . . . . . . . . . . . . . . . . . . . 62 XII Transferring Selections Between Images . . . . . . . . . . . . . . . . . . . . . . . 64 XIII Converting Composite Selections . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 XIV Applying Auto Brightness/Contrast to Entire Stacks . . . . . . . . . . . . . . . . 76 XV Display Range of DICOM Images . . . . . . . . . . . . . . . . . . . . . . . . . . . 78 XVI Brightness/Contrast of High Bit–Depth Images . . . . . . . . . . . . . . . . . . . 79 XVII Embedding Color Annotations in Grayscale Images . . . . . . . . . . . . . . . . . 86 XVIII Working with Zoomed Canvases . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 XIX Hexadecimal Color Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103 XX Creating Binary Masks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113 XXI Skeletonize vs Skeletonize 3D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115 XXII Interpreting Binary Images . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118 XXIII Global Calibrations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141 XXIV Using Scanners in Densitometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144 XXV Selecting ROIs in the ROI Manager . . . . . . . . . . . . . . . . . . . . . . . . . . 153 XXVI Focus on Bioimage Informatics . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173 viii

Macro listing 1 Replace Red with Magenta ijm(Using ProcessD Image Calculator.) 2 Replace Red with Magenta ijm(Using Image b Color b Channels.) 17 3 Ensuring Specific Settings at Launch 4 Customizing the Image Popup Menu 5 Customizing the Float Behavior of I's Main Window 6 Setting Fileb Open Samples for Offline Usage 7 Using a Keyboard Shortcut to Change Selection Color 8 Obtaining Histogram Lists 142 9 Assigning Keyboard Shortcuts to Image Tools 169 10 Cycling Through the Toolbar Using Keyboard Shortcuts 170 11 Temporary Activation of a Tool

Macro Listings 1 Replace Red with Magenta.ijm (Using Process . Image Calculator. . .) . . . . . . . . 17 2 Replace Red with Magenta.ijm (Using Image . Color . Channels. . .) . . . . . . . . . 17 3 Ensuring Specific Settings at Launch . . . . . . . . . . . . . . . . . . . . . . . . . 22 4 Customizing the Image Popup Menu . . . . . . . . . . . . . . . . . . . . . . . . . 42 5 Customizing the Float Behavior of IJ’s Main Window . . . . . . . . . . . . . . . 47 6 Setting File . Open Samples . for Offline Usage . . . . . . . . . . . . . . . . . . . . 51 7 Using a Keyboard Shortcut to Change Selection Color . . . . . . . . . . . . . . . 70 8 Obtaining Histogram Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142 9 Assigning Keyboard Shortcuts to ImageJ Tools . . . . . . . . . . . . . . . . . . . 169 10 Cycling Through the Toolbar Using Keyboard Shortcuts . . . . . . . . . . . . . . 170 11 Temporary Activation of a Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170 ix

Guide formats This guide is available in the following formats Enhanced PDF Optimized for electronic viewing and highly enriched in hypertext links(see ConventionsUsedinthisGuide).Availableathttp://imagej.nihgov/ij/docs/guide/ user-guide. pe Htmldocumentavailableonlineathttp://imagej.nihgov/ij/docs/guide/.Forofflineus ageadownloadableZiparchiveisalsoavailableathttp://imagej.nihgov/ij/docs/ Printable booklets Two-sided booklets that can be printed on a duplex unit printer by setting the automatic duplex mode to"short edge binding,. Two formats are available A4(http://imagej.nihgov/ij/docs/guide/user-guide-a4booklet.pdf)andlettersize paper(http://imagej.nihgov/ij/docs/guide/user-guide-usbooklet.pdf) Conventions Used in this guide Throughout the guide, internal links are displayed in gray(e. g, Part IV Image J User Interface) LinkstoexternalUrls,suchastheImagejwebsitehttp://imagej.nihgov/ij/,aredisplayedin dark blue ImageJ commands are typed in sans serif typeface with respective shortcut keys ranked by square brackets(e. g. ImageD Duplicate .. [DD. As explained in Using Keyboard Shortcuts, this notation implies Shift-modifiers(i.e, [D] means pressing Shift). [d] only the]key)and ssumes that Require control key for shortcuts in Editb Options b Misc... is unchecked. Note that references to the ctrl key include the aB Cmd key of Macintosh keyboards Useful tips and reminders are placed in ' Noteworthy notes'numbered with upper case roman numerals(e. g, I Frontmost Window and Window Activation). The full list of these notes is File directories and file extensions are typed in monospaced font marked by a related icon, e. g, file EStartupMacros txt in folder a/Applications/ImageJ/macros/ Macro functions and code snippets are typed in monospaced font, e. g, resetMinAndMaxO Scripts and macros are numbered with arabic numerals included in parentheses(e.g,(2) Replace Red with Magenta ijm(Using Image b Color b Channels.) on page 17) and typeset with the same syntax markup provided by the Fiji Script Editor. The full list of macro listings is on pa Selected highlights of version 1. 46r are listed on page vii and fagged with colored marginal notes These should be interpreted as JEW IN A new feature implemented in Image J146r A routine that has been improved since previous versions. Typically, a faster or more precise algorithm, a command with better usability, or a task that has been extended to more image types. A pre-existing command that has been renamed or moved to a different menu location in Image 1.46r

Guide Formats This guide is available in the following formats: Enhanced PDF Optimized for electronic viewing and highly enriched in hypertext links (see Conventions Used in this Guide). Available at http://imagej.nih.gov/ij/docs/guide/ user-guide.pdf. HTML document available online at http://imagej.nih.gov/ij/docs/guide/. For offline us￾age a downloadable ZIP archive is also available at http://imagej.nih.gov/ij/docs/ user-guide.zip. Printable booklets Two-sided booklets that can be printed on a duplex unit printer by setting the automatic duplex mode to “short edge binding”. Two formats are available: A4 (http://imagej.nih.gov/ij/docs/guide/user-guide-A4booklet.pdf) and letter size paper (http://imagej.nih.gov/ij/docs/guide/user-guide-USbooklet.pdf). Conventions Used in this Guide Throughout the guide, internal links are displayed in gray (e.g., Part IV ImageJ User Interface). Links to external URLs, such as the ImageJ website, http://imagej.nih.gov/ij/, are displayed in dark blue. ImageJ commands are typed in sans serif typeface with respective shortcut keys flanked by square brackets (e.g.: Image . Duplicate. . . [D]). As explained in Using Keyboard Shortcuts, this notation implies Shift-modifiers (i.e., [D] means pressing Shift D , [d] only the D key) and assumes that Require control key for shortcuts in Edit . Options . Misc. . . is unchecked. Note that references to the Ctrl key include the Cmd key of Macintosh keyboards. Useful tips and reminders are placed in ‘Noteworthy notes’ numbered with upper case roman numerals (e.g., I Frontmost Window and Window Activation). The full list of these notes is available on page viii. Filenames, directories and file extensions are typed in monospaced font marked by a related icon, e.g., file StartupMacros.txt in folder /Applications/ImageJ/macros/. Macro functions and code snippets are typed in monospaced font, e.g., resetMinAndMax(). Scripts and macros are numbered with arabic numerals included in parentheses (e.g., (2) Replace Red with Magenta.ijm (Using Image . Color . Channels. . .) on page 17) and typeset with the same syntax markup provided by the Fiji Script Editor. The full list of macro listings is available on page ix. Selected highlights of version 1.46r are listed on page vii and flagged with colored marginal notes. These should be interpreted as: New in IJ 1.46r A new feature implemented in ImageJ 1.46r. Improved in IJ 1.46r A routine that has been improved since previous versions. Typically, a faster or more precise algorithm, a command with better usability, or a task that has been extended to more image types. Changed in IJ 1.46r A pre-existing command that has been renamed or moved to a different menu location in ImageJ 1.46r