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ImageJ User Guide IJ 1.45m ImageJ User Guide IJ 1.45m Tiago Ferreira • Wayne Ra

ImageJ User Guide IJ 1.45m ImageJ User Guide IJ 1.45m Tiago Ferreira • Wayne Rasband December 27, 2011 Foreword The ImageJ User Guide provides a detailed overview of ImageJ (and inherently Fiji), the standard in scientiﬁc image analysis. 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 ﬁles are available 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 resources (see Getting Involved). Contents Release Notes for ImageJ 1.45m vii Noteworthy viii Macro Listings ix Guide Conventions x I Getting Started 1 What is ImageJ? 1 2 Installing and Maintaining ImageJ 2 2.1 ImageJ Distributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 2.2 Software Packages Built on Top of ImageJ . . . . . . . . . . . . . . . . . . . . 3 2.3 ImageJ2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 3 Getting Help 4 3.1 Help on Image Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 3.2 Help on ImageJ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 II Working with ImageJ 4 Using Keyboard Shortcuts 8 5 Finding Commands 9 6 Undo and Redo 9 7 Image Types and Formats 10 8 Stacks, Virtual Stacks and Hyperstacks 11 9 Color Images 13 10 Selections 17 11 Settings and Preferences 19 III Extending ImageJ 12 Macros 20 13 Scripts 21 14 Plugins 21 15 Scripting in Other Languages 22 16 Running ImageJ From the Command Line 23 ii 17 ImageJ Interoperability 24 IV ImageJ User Interface 18 Tools 18.1 Area Selection Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 18.2 Line Selection Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 18.3 Arrow Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 18.4 Angle Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 18.5 Point Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 18.6 Multi-point Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 18.7 Wand Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 18.8 Text Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 18.9 Magnifying Glass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 18.10 Scrolling Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 18.11 Color Picker . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 18.12 Toolset Switcher . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 18.13 Macro Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 19 Contextual Menu 34 20 Results Table 35 21 ImageJ Editor 36 22 Log Window 38 V Menu Commands 23 File ▷ 40 23.1 New ▷. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 23.2 Open. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 23.3 Open Next [O] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 23.4 Open Samples ▷ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41 23.5 Open Recent ▷. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 23.6 Import ▷ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42 23.7 Close [w] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 23.8 Close All . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 23.9 Save [s] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 23.10 Save As ▷. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 23.11 Revert [r] . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 23.12 Page Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 23.13 Print. . . [p] . . . . . . . . . . . . . . . . . . . uploads/Litterature/ user-guide - 2023-05-30T231030.102.pdf