Imagej User Guide Contents Release Notes for Imagej 1.46R Vii IJ 1.46R Noteworthy Viii
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RevisedIJ 1.46r edition ImageJ UserUser Guide Guide ImageJImageJ/Fiji 1.46 ImageJ User Guide Contents Release Notes for ImageJ 1.46r vii IJ 1.46r Noteworthy viii Tiago Ferreira • Wayne Rasband IJ User Guide | Booklet 1 Macro Listings ix Conventions x I Getting Started 1 Introduction 1 2 Installing and Maintaining ImageJ2 2.1 ImageJDistributions.................................. 2 2.2 Related Software ................................... 3 2.3 ImageJ2 ........................................ 5 3 Getting Help5 3.1 Help on Image Analysis................................ 5 3.2 Help on ImageJ.................................... 6 II Working with ImageJ 4 Using Keyboard Shortcuts8 5 Finding Commands8 6 Undo and Redo9 7 Image Types and Formats 10 Tuesday 2nd October, 2012 8 Stacks, Virtual Stacks and Hyperstacks 12 9 Color Images 14 10 Selections 17 Foreword 10.1 Manipulating ROIs .................................. 18 10.2 Composite Selections................................. 19 The ImageJ User Guide provides a detailed overview of ImageJ (and inherently Fiji), 10.3 Selections With Sub-pixel Coordinates ....................... 19 the standard in scientific image analysis (see XXVI Focus on Bioimage Informatics). It was thought as a comprehensive, fully-searchable, self-contained, annotatable 11 Overlays 19 manual (see Conventions Used in this Guide). A HTML version is also available as 12 3D Volumes 21 well as printer-friendly booklets (see Guide Formats). Its latest version can always be obtained from http://imagej.nih.gov/ij/docs/guide. The source files are available 13 Settings and Preferences 22 through a Git version control repository at http://fiji.sc/guide.git. Given ImageJ’s heavy development this guide will always remain incomplete. All Im- ageJ users and developers are encouraged to contribute to the ImageJ documentation III Extending ImageJ resources (see Getting Involved). 14 Macros 23 ii 15 Scripts 24 26.2 Open. [o] ....................................... 50 26.3 Open Next [O] ..................................... 50 16 Plugins 24 26.4 Open Samples . .................................... 50 26.5 Open Recent . ..................................... 51 17 Scripting in Other Languages 26 26.6 Import . ........................................ 51 18 Running ImageJ From the Command Line 26 26.7 Close [w] ........................................ 55 26.8 Close All ........................................ 55 26.9 Save [s] ......................................... 56 IV ImageJ User Interface 26.10 Save As . ........................................ 56 26.11 Revert [r] ........................................ 60 19 Tools 26.12 Page Setup. ..................................... 60 19.1 Area Selection Tools ................................. 29 26.13 Print. [p] ....................................... 60 19.2 Line Selection Tools.................................. 31 26.14 Quit ........................................... 60 19.3 Arrow Tool....................................... 32 19.4 Angle Tool....................................... 33 27 Edit . 61 19.5 Point Tool....................................... 33 27.1 Undo [z] ........................................ 61 19.6 Multi-point Tool.................................... 34 27.2 Cut [x] ......................................... 61 19.7 Wand Tool....................................... 34 27.3 Copy [c] ......................................... 61 19.8 Text Tool ....................................... 35 27.4 Copy to System .................................... 61 19.9 Magnifying Glass ................................... 36 27.5 Paste [v] ........................................ 61 19.10 Scrolling Tool ..................................... 36 27.6 Paste Control. .................................... 61 19.11 Color Picker Tool................................... 36 27.7 Clear .......................................... 62 19.12 More Tools Menu................................... 37 27.8 Clear Outside ...................................... 62 19.13 Arrow ......................................... 38 27.9 Fill [f] .......................................... 62 19.14 Brush.......................................... 38 27.10 Draw [d] ........................................ 62 19.15 Developer Menu.................................... 38 27.11 Invert [I] ........................................ 63 19.16 Flood Filler ...................................... 39 27.12 Selection . ....................................... 63 19.17 LUT Menu....................................... 39 27.13 Options . ........................................ 68 19.18 Overlay Brush..................................... 39 28 . 75 19.19 Pencil.......................................... 40 Image . 19.20 Pixel Inspector .................................... 40 28.1 Type ......................................... 75 . 19.21 Spray Can....................................... 41 28.2 Adjust ........................................ 75 19.22 Stacks Menu...................................... 41 28.3 Show Info. [i] .................................... 82 28.4 Properties. [P] .................................... 83 20 Custom Tools 41 28.5 Color . ......................................... 83 28.6 Stacks . ........................................ 86 21 Contextual Menu 42 28.7 Hyperstacks . ..................................... 96 28.8 Crop [X] ........................................ 97 22 Results Table 43 28.9 Duplicate. [D] .................................... 97 28.10 Rename. ....................................... 98 23 Editor 44 28.11 Scale. [E] ....................................... 98 . 24 Log Window 46 28.12 Transform ...................................... 98 28.13 Zoom . .........................................100 25 Customizing the ImageJ Interface 46 28.14 Overlay . ........................................101 28.15 Lookup Tables . ....................................105 25.1 Floating Behavior of Main Window......................... 46 IJ User Guide | Booklet 2 25.2 Pointer......................................... 47 29 Process . 107 29.1 Smooth [S] .......................................107 V Menu Commands 29.2 Sharpen .........................................107 29.3 Find Edges .......................................107 26 File . 49 29.4 Find Maxima. ....................................107 26.1 New . .......................................... 49 29.5 Enhance Contrast. ..................................109 iii iv 29.6 Noise . .........................................110 33.12 About Plugins . ....................................165 29.7 Shadows . .......................................111 33.13 About ImageJ. ....................................165 29.8 Binary . ........................................112 29.9 Math . .........................................117 29.10 FFT . ..........................................120 VI Keyboard Shortcuts 29.11 Filters . .........................................124 IJ User Guide | Booklet 3 29.12 Batch . .........................................126 34 Key Modifiers 29.13 Image Calculator. ..................................128 34.1 Alt Key Modifications ................................167 29.14 Subtract Background. ................................129 34.2 Shift Key Modifications................................168 29.15 Repeat Command [R] .................................131 34.3 Ctrl (or Cmd) Key Modifications ..........................169 34.4 Space Bar .......................................169 30 Analyze . 132 34.5 Arrow Keys ......................................169 30.1 Measure. [m] .....................................132 30.2 Analyze Particles. ..................................132 35 Toolbar Shortcuts 30.3 Summarize .......................................135 Credits 171 30.4 Distribution. .....................................135 30.5 Label ..........................................136 ImageJ Related Publications 174 30.6 Clear Results ......................................136 30.7 Set Measurements. .................................136 List of Abbreviations and Acronyms 181 30.8 Set Scale. ......................................139 30.9 Calibrate. ......................................139 Index 182 30.10 Histogram [h] ......................................140 30.11 Plot Profile [k] .....................................142 Colophon 186 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