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User guide 35 IJ r ImageJ UUsseerr GGuuiiddee ImageJ ImageJ Fiji ImageJ User Guide IJ r Tiago Ferreira ? Wayne Rasband Thursday th July Foreword The ImageJ User Guide provides a detailed overview of ImageJ and inherently Fiji the standard in scienti ?c im

IJ r ImageJ UUsseerr GGuuiiddee ImageJ ImageJ Fiji ImageJ User Guide IJ r Tiago Ferreira ? Wayne Rasband Thursday th July Foreword The ImageJ User Guide provides a detailed overview of ImageJ and inherently Fiji the standard in scienti ?c image analysis see XXVI Focus on Bioimage Informatics It was thought as a comprehensive fully-searchable self-contained annotatable manual see Conventions Used in this Guide A HTML version is also available as 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 ?les are available through a Git version control repository at http ?ji sc guide git Given ImageJ ? s heavy development this guide will always remain incomplete All ImageJ users and developers are encouraged to contribute to the ImageJ documentation resources see Getting Involved Contents Release Notes for ImageJ r vii Noteworthy viii Macro Listings ix Conventions x I Getting Started Introduction Installing and Maintaining ImageJ ImageJDistributions Related Software ImageJ Getting Help Help on Image Analysis Help on ImageJ II Working with ImageJ Using Keyboard Shortcuts Finding Commands Undo and Redo Image Types and Formats Stacks Virtual Stacks and Hyperstacks Color Images Selections Manipulating ROIs Composite Selections Selections With Sub-pixel Coordinates Overlays D Volumes Settings and Preferences III Extending ImageJ Macros ii Scripts Plugins Scripting in Other Languages Running ImageJ From the Command Line IV ImageJ User Interface Tools Area Selection Tools Line Selection Tools Arrow Tool Angle Tool Point Tool Multi-point Tool Wand Tool Text Tool Magnifying Glass Scrolling Tool Color Picker Tool More Tools Menu Arrow Brush Developer Menu Flood Filler LUT Menu Overlay Brush Pencil Pixel Inspector Spray Can Stacks Menu Custom Tools Contextual Menu Results Table Editor Log Window Customizing the ImageJ Interface Floating Behavior of Main Window Pointer V Menu Commands File New iii Open o Open Next O Open Samples Open Recent Import Close w Close All Save s Save As Revert r Page Setup Print p Quit Edit Undo z Cut x Copy c Copy to System Paste v Paste Control Clear Clear Outside Fill f Draw d Invert I Selection Options Image Type Adjust Show Info i Properties P Color Stacks Hyperstacks Crop X Duplicate D Rename Scale E Transform Zoom Overlay Lookup Tables Process Smooth S Sharpen Find Edges Find Maxima Enhance Contrast iv Noise Shadows Binary Math FFT Filters Batch Image Calculator Subtract Background Repeat Command R Analyze Measure m Analyze Particles Summarize Distribution Label Clear Results Set Measurements Set Scale Calibrate Histogram h Plot Pro ?le k Surface Plot Gels Tools Plugins Macros Shortcuts Utilities New Compile and Run Window Show All Put Behind tab Cascade Tile Help ImageJ Website ImageJ News Documentation Installation Mailing List Dev Resources Plugins Macros Macro Functions Update ImageJ Refresh Menus v About Plugins About ImageJ VI Keyboard Shortcuts Key Modi ?ers Alt Key Modi ?cations Shift Key Modi ?cations Ctrl or Cmd Key Modi ?cations Space Bar Arrow Keys Toolbar Shortcuts Credits ImageJ Related Publications List of Abbreviations