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 usage 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