Web site of Digital Image Processing: An Algorithmic Introduction using Java by wilhelm and Mark Burge [11]. This technical book provides a modern, self-contained,intro- duction to digital image processing techniques. Numerous complete Java implementations are provided, all of which work within ImageJ Hypermedia Image Processing Reference(HIPR2) Developed at the Department of Artificial Intelligence in the University of Edinburgh provides on-line reference and tutorial information on a wide range of image processing operations IFN wikipage The Imaging Facility Network(IFN) in Biopolis Dresden provides access to advanced microscopy systems and image processing. The website hosts high quality teaching material and useful links to external resources stereology. info Stereology Information for the Biological Sciences, designed to introduce both basic and dvanced concepts in the field of stereology SEE ALSO: ImageJ Related Publications on page 174 3.2 Help on imageJ Below is a list of the ImageJ help resources that complement this guide(see Guide Formats) Specific documentation on advanced uses of ImageJ(macro programming, plugin development etc. )is discussed in Extending ImageJ 1. The Image J online documentation pages Can be accessed via the help Documentation . command http://fiji.sc, 3. The ImageJ Information and Documentation Portal(Image J wikipage) http://imagejdocu.tudor.lu/doku.ph 4. Video tutorials on the ImageJ Documentation Portal and the Fiji You Tube channel: http://imagejdocu.tudorIu/doku.phpid=video:start&sl=videoandhttp://www.youtub com/ user/fijichannel. New ImageJ users will probably profit from Christine Labno's video 5. The ImageJ for Microscopy manual http://www.macbiophotonics.ca/imagej/ 6. Several online documents. most of them listed at http://imagej.nih.gov/ij/links.htmlandhttp://imagej.nih.gov/ij/docs/e 7. Mailing lists: (a) imagej-Http: //imagej. nih. gov/ij/list.html General user and developer discussion about Image J Can be accessed via the help iling List... command. This list is also mirrored at Nabble and gmane. You may find it easier to search and browse the list archives on these mirrors. Specially useful are the RSS feeds and the frames and threads view provided by gmane Last updated: 2012/10/02
Getting Help Help on ImageJ – imagingbook.com Web site of Digital Image Processing: An Algorithmic Introduction using Java by Wilhelm Burger and Mark Burge [11]. This technical book provides a modern, self-contained, introduction to digital image processing techniques. Numerous complete Java implementations are provided, all of which work within ImageJ. – Hypermedia Image Processing Reference (HIPR2) Developed at the Department of Artificial Intelligence in the University of Edinburgh, provides on-line reference and tutorial information on a wide range of image processing operations. – IFN wikipage The Imaging Facility Network (IFN) in Biopolis Dresden provides access to advanced microscopy systems and image processing. The website hosts high quality teaching material and useful links to external resources. – stereology.info Stereology Information for the Biological Sciences, designed to introduce both basic and advanced concepts in the field of stereology. See also: ImageJ Related Publications on page 174 3.2 Help on ImageJ Below is a list of the ImageJ help resources that complement this guide (see Guide Formats). Specific documentation on advanced uses of ImageJ (macro programming, plugin development, etc.) is discussed in Extending ImageJ. 1. The ImageJ online documentation pages Can be accessed via the Help . Documentation. . . command. 2. The Fiji webpage: http://fiji.sc/ 3. The ImageJ Information and Documentation Portal (ImageJ wikipage): http://imagejdocu.tudor.lu/doku.php 4. Video tutorials on the ImageJ Documentation Portal and the Fiji YouTube channel: http://imagejdocu.tudor.lu/doku.php?id=video:start&s[]=video and http://www.youtube. com/user/fijichannel. New ImageJ users will probably profit from Christine Labno’s video tutorial. 5. The ImageJ for Microscopy manual http://www.macbiophotonics.ca/imagej/ 6. Several online documents, most of them listed at: http://imagej.nih.gov/ij/links.html and http://imagej.nih.gov/ij/docs/examples/ 7. Mailing lists: (a) ImageJ — http://imagej.nih.gov/ij/list.html General user and developer discussion about ImageJ. Can be accessed via the Help . Mailing List. . . command. This list is also mirrored at Nabble and Gmane. You may find it easier to search and browse the list archives on these mirrors. Specially useful are the RSS feeds and the frames and threads view provided by Gmane. 6 Last updated: 2012/10/02
(b)fijiusers-http://groups.googlecom/group/fiji-users For user discussion specific to Fiji (rather than core Image J) (c)fiji-deVel-http://groups.googlecom/group/fiji-devel For developer discussion specific to Fiji (d)imagej-dEvel-http://imagejdev.org/mailman/listinfo/imagej-devel For communication and coordination of the Image Dev project (e) Dedicated mailing lists for ImageJ related projects Describedathttp://imagejdev.org/mailing-lists USing Mailing-lists If you are having problems with ImageJ, you should inquiry about them in the appropriated list The ImageJ mailing list is an unmoderated forum subscribed by a knowledgeable worldwide user community with 2000 advanced users and developers. To have your questions promptly answered you should consider the following: Read the documentation files(described earlier in this section) before posting. Because there will always be a natural lag between the implementation of key features and their documentation it may be wise to check briefly the ImageJ news website(HelpD ImageJ 2. Look up the mailing list archives(Helpb Mailing List .). Most of your questions may have already been answered 3. If you think you are facing a bug try to upgrade to the latest version of Image J(Help Update ImageJ.). You should also check if you are running the latest version of the Java Virtual Machine for your operating system. Detailed instructions on how to submit a bug reportarefoundathttp://imagej.nihgov/ij/docs/faqs.html#bug 4. Remember that in most cases you can find answers within your own ImageJ installation without even connecting to the internet since the heuristics for finding commands or writin macros have been significantly improved in later versions(see Finding Commands and Extending ImageJ) As with any other mailing list, you should always follow basic netiquette, namely (a) Use descriptive subject lines- Re: Problem with Image >Set Scale command is much more effective than a general Re: Problem (b) Stay on topic- Do not post off-topic messages, unrelated to the message thread (c) Be careful when sending attachments- Refrain from attaching large files. Use, e.g,a (d) Edit replies- You should include only the minimum content that is necessary to provide a logical flow from the question to the answer, i.e., quote only as much as bsolutely necessary and relevant Last updated: 2012/10/02
Getting Help Help on ImageJ (b) Fiji users — http://groups.google.com/group/fiji-users For user discussion specific to Fiji (rather than core ImageJ). (c) Fiji-devel — http://groups.google.com/group/fiji-devel For developer discussion specific to Fiji. (d) ImageJ-devel — http://imagejdev.org/mailman/listinfo/imagej-devel For communication and coordination of the ImageJDev project. (e) Dedicated mailing lists for ImageJ related projects Described at http://imagejdev.org/mailing-lists . Using Mailing-lists If you are having problems with ImageJ, you should inquiry about them in the appropriated list. The ImageJ mailing list is an unmoderated forum subscribed by a knowledgeable worldwide user community with ≈2000 advanced users and developers. To have your questions promptly answered you should consider the following: 1. Read the documentation files (described earlier in this section) before posting. Because there will always be a natural lag between the implementation of key features and their documentation it may be wise to check briefly the ImageJ news website (Help . ImageJ News. . .). 2. Look up the mailing list archives (Help . Mailing List. . .). Most of your questions may have already been answered. 3. If you think you are facing a bug try to upgrade to the latest version of ImageJ (Help . Update ImageJ. . .). You should also check if you are running the latest version of the Java Virtual Machine for your operating system. Detailed instructions on how to submit a bug report are found at http://imagej.nih.gov/ij/docs/faqs.html#bug. 4. Remember that in most cases you can find answers within your own ImageJ installation without even connecting to the internet since the heuristics for finding commands or writing macros have been significantly improved in later versions (see Finding Commands and Extending ImageJ). 5. As with any other mailing list, you should always follow basic netiquette, namely: (a) Use descriptive subject lines – Re: Problem with Image>Set Scale command is much more effective than a general Re: Problem. (b) Stay on topic – Do not post off-topic messages, unrelated to the message thread. (c) Be careful when sending attachments – Refrain from attaching large files. Use, e.g., a file hosting service instead. (d) Edit replies – You should include only the minimum content that is necessary to provide a logical flow from the question to the answer, i.e., quote only as much as absolutely necessary and relevant. 7 Last updated: 2012/10/02
Part I Working with imageJ This part introduces some basic aspects of ImageJ so that you can use the software more efficiently. It also introduces some important terms and concepts used throughout this guide You may skip it if you already use the program efficiently and are familiar with te rims su as Virtual Stacks, Hyperstacks, Pseudocolor Images, Color Composite Images or Composite Selections 4 Using Keyboard Shortcuts You'll learn more and more shortcut keys as you use ImageJ, because(almost )all shortcuts are listed throughout ImageJ menus. Similarly, in this guide each command has its shortcut key listed on its name(flanked by square brackets). Please note that the notation for these means Shift-A)and assumes that Require control key for shortcuts in Edit D Options D Mis: 7 key-bindings is case sensitive, i. e, Shift-modifiers are not explicitly mentioned(a capital is unchecked (i.e, except when using the IJ Editor or the Text Tool, you won't have to hold down the Control key to use menu shortcuts). For example, the command Edit b Invert [can be evoked by Shift)[Ior Ctrl) Shift)(I if Require control key for shortcuts is checked. The full list of Image J shortcuts(see Keyboard Shortcuts)can be retrieved at any time using the lugins b Utilities b List Shortcuts.. command There are three modifier keys in ImageJ Control (Command Key on Apple keyboards)Denoted by 'Ctrl'or [ Ctrl) in this document Although a control key is typically present on Apple keyboards, on a Macintosh computer running ImageJ the Command key 9B Cmd replaces the functionality of the Control key of other operating systems. For sake of simplification, 'Ctrl will always refer to both throughout this guide Shift Denoted by" or Shift] in this document Denoted by 'Alt'or Alt]in this document. This is also the Option'or'Meta'key on many keyboards. In ImageJ, it is also used to type special unit symbols such as p (Alt M) or A(Alt ShiftA J) SEE ALSO: Keyboard Shortcuts, Plugins b Shortcuts 5 Finding Commands Navigating through the extensive list of ImageJ commands, macros and plugins may be quite cumbersome. Through its built-in Command Finder/Launcher[ 48, ImageJ offers an expe- dite alternative that allows you to retrieve commands extremely fast: Plugins Utilities D Find commands In addition, ImageJ features a find function that locates macros, scripts and plugins source (E. java)files on your computer: the Plugins b Utilities D Search.. command. Because most of IJ source files contain circumstanced comments, you can use this utility to retrieve files
Part II Working with ImageJ This part introduces some basic aspects of ImageJ so that you can use the software more efficiently. It also introduces some important terms and concepts used throughout this guide. You may skip it if you already use the program efficiently and are familiar with terms such as Virtual Stacks, Hyperstacks, Pseudocolor Images, Color Composite Images or Composite Selections. 4 Using Keyboard Shortcuts You’ll learn more and more shortcut keys as you use ImageJ, because (almost) all shortcuts are listed throughout ImageJ menus. Similarly, in this guide each command has its shortcut key listed on its name (flanked by square brackets). Please note that the notation for these key-bindings is case sensitive, i.e., Shift-modifiers are not explicitly mentioned (a capital A means Shift–A) and assumes that Require control key for shortcuts in Edit . Options . Misc. . . is unchecked (i.e., except when using the IJ Editor or the Text Tool, you won’t have to hold down the Control key to use menu shortcuts). For example, the command Edit . Invert [I] can be evoked by Shift I or Ctrl Shift I if Require control key for shortcuts is checked. The full list of ImageJ shortcuts (see Keyboard Shortcuts) can be retrieved at any time using the Plugins .Utilities . List Shortcuts. . . command. There are three modifier keys in ImageJ: Control (Command Key on Apple keyboards) Denoted by ‘Ctrl’ or Ctrl in this document. Although a control key is typically present on Apple keyboards, on a Macintosh computer running ImageJ the Command key Cmd replaces the functionality of the Control key of other operating systems. For sake of simplification, ‘Ctrl’ will always refer to both throughout this guide. Shift Denoted by ‘Shift’ or Shift in this document. Alt Denoted by ‘Alt’ or Alt in this document. This is also the ‘Option’ or ‘Meta’ key on many keyboards. In ImageJ, it is also used to type special unit symbols such as µ ( Alt M ) or Å ( Alt Shift A ). See also: Keyboard Shortcuts, Plugins . Shortcuts . 5 Finding Commands Navigating through the extensive list of ImageJ commands, macros and plugins may be quite cumbersome. Through its built-in Command Finder / Launcher[48], ImageJ offers an expedite alternative that allows you to retrieve commands extremely fast: Plugins .Utilities . Find Commands. . . [l]. In addition, ImageJ features a find function that locates macros, scripts and plugins source ( .java) files on your computer: the Plugins .Utilities . Search. . . command. Because most of IJ source files contain circumstanced comments, you can use this utility to retrieve files 8
Undo and redo I FRONTMOST WINDOW AND WINDOW ACTIVATIO In ImageJ, all operations are performed on the active(frontmost)image(which has its title bar highlighted). If a window is already open it will activate when its opening command is re-run e.g., if the B&C window is already opened(Image D Adjust D Brightness/Contrast..[C]), pressing its keyboard shortcut( Shift C D) will activate it Pressing Enter on any image will bring the Main ImageJ window to the foreground. In addition it is also possible to permanently place the main window above all other windows(see Floating Behavior of Main Window) Plugins D Utilities b Find Commands.. U 1600 Command Finder Type part of a cor th Adaptive 3 DThreshold ColocalisationThreshold Color Threshold DynamicThreshold Id 60 Search Entropy Threshold B Show full information M Close when running Threshold M Search contents Mignore case M search macros folder O Search plugins folder Loa O Search scripts folder B Search source folder agel/macros /Auto ThresholdAndSegment tx ImageJ/macros/examples /Auto Thresholding Demo. txt (Cancel( Ok (]/macros/examples/SetOverUnderThresholdColorstxt Plugins b Utilities b Search related not only to a image processing routine(e.g, background or co-localization) but also to a practical context such as radiogram, cell or histology. Indeed, ImageJ source files contain detailed annotations useful to both developers and regular users that want to know more about ImageJ routines and algorithm Search.. and Find Commands..[ are described in detail in Plugins p UtilitiesD searches for a menu entry and retrieves the source file of the respective comany oa SEE ALSO: Control Panel..[U, Keyboard Shortcuts and E SourceCodeRetriever, a macro tha 6 Undo and redo Probably the first thing you will notice is that Image does not have a large undo/redo buffer Undo(Edit b Undo [z))is currently limited to the most recent image editing /filtering operation With time you will appreciate that this is necessary to minimize memory overhead. Nevertheless with IJ 1.45 and later, Undo [z is, in most cases, undoable and can be applied to multiple images if Keep multiple undo buffers is checked in Editb Options b Memory Threads If you cannot recover from a mistake, you can always use Fileb Revert [] to reset the image lo its last saved state. For selections, Edit b Selection b Restore Selection [E] can be used to recover any misdeal selectio Last updated: 2012/10/02
Undo and Redo I Frontmost Window and Window Activation In ImageJ, all operations are performed on the active (frontmost) image (which has its title bar highlighted). If a window is already open it will activate when its opening command is re-run, e.g., if the B&C window is already opened (Image . Adjust . Brightness/Contrast. . . [C]), pressing its keyboard shortcut ( Shift C ) will activate it. Pressing Enter on any image will bring the Main ImageJ window to the foreground. In addition, it is also possible to permanently place the main window above all other windows (see Floating Behavior of Main Window). Plugins .Utilities . Find Commands. . . [l] Plugins .Utilities . Search. . . related not only to a image processing routine (e.g., background or co-localization) but also to a practical context such as radiogram, cell or histology. Indeed, ImageJ source files contain detailed annotations useful to both developers and regular users that want to know more about ImageJ routines and algorithms. Search. . . and Find Commands. . . [l] are described in detail in Plugins .Utilities . . See also: Control Panel. . . [U], Keyboard Shortcuts and SourceCodeRetriever, a macro that searches for a menu entry and retrieves the source file of the respective command 6 Undo and Redo Probably the first thing you will notice is that ImageJ does not have a large undo/redo buffer. Undo (Edit .Undo [z]) is currently limited to the most recent image editing / filtering operation. With time you will appreciate that this is necessary to minimize memory overhead. Nevertheless, with IJ 1.45 and later, Undo [z] is, in most cases, undoable and can be applied to multiple images if Keep multiple undo buffers is checked in Edit . Options . Memory & Threads. . . If you cannot recover from a mistake, you can always use File . Revert [r] to reset the image lo its last saved state. For selections, Edit . Selection . Restore Selection [E] can be used to recover any misdealt selection. 9 Last updated: 2012/10/02
Image Types and Formats In ImageJ the equivalent to" Redo' is the Process b Repeat Command R], that re-runs the previous used command(skipping Edit D Undo [z] and Fileb Open..[o] commands) SEE ALSO: Plugins D Utilities b Reset ., Multi Undo plugin 7 Image Types and Formats Digital Images are two-dimensional grids of pixel intensities values with the width and height of the image being defined by the number of pixels in a(rows) and y(columns)direction. Thus, pixels (picture elements) are the smallest single components of images, holding numeric values pixel intensities- that range between black and white. The characteristics of this range, i.e the number of unique intensity(brightness) values that can exist in the image is defined as the bit-depth of the image and specifies the level of precision in which intensities are coded, e.g.: A 2-bit image has 22= 4 tones: 00(black), 01(gray), 10(gray), and 11(white). A 4-bit image has 24= 16 tones ranging from 0000(0)to 1111(16), etc. In terms of bits per pixel(bpp), the most frequent types of images(ImageD Type)that ImageJ deals with are(Image J2 supports many more types of image data) 8-bit Images that can display 256(2)gray levels(integers only) 16-bit Images that can display 65, 536(2b) gray levels(integers only 32-bit Images that can display 4, 294, 967, 296(232) gray levels(real numbers).In 32-bit images, pixels are described by floating point values and can have ANY intensity value including NaN(Not a Number) RGB Color Color Images that can display 256 values in the Red, Green and Blue channel These are 24-bit(2x8)images. RGB color images can also be 32-bit color images (24-bit color images with additional eight bits coding alpha blending values, i.e transparency) Native formats Natively (i.e. without the need of third-party plugins) Image J opens the following formats: TIFF GIF JPEG. PNG. DICOM IP, PGM and FITS. Many more formats are supported with the aid of plugins. These are discussed in Non-native Formats TIFF (Tagged Image File Format)is the 'default' format of ImageJ(cf. FileD Save [s)) Images can be 1-bit, 8-bit, 16-bit(unsigned), 32-bit(real)or RGB color. TIFF files with multiple images of the same type and size open as Stacks or Hyperstacks ImageJ opens lossless compressed TIFF files(see II Image Types: Lossy Compression and Metadata) by the LZW, Pack Bits and ZIP(Deflate/Inflate)[2 compression schemes. In addition, TIFF files can be opened and saved as Zip archives Tiff tags and information needed to import the file(number of images, offset to first images, gap between images)are printed to the Log Window when ImageJ is running in Debug Mode(Edit b Options D Misc., see Settings and Preferences) A numeric variable is signed if it can represent both positive and negative numbers, and unsigned if it can only represent positive numbers Last updated: 2012/10/02
Image Types and Formats In ImageJ the equivalent to ‘Redo’ is the Process . Repeat Command [R], that re-runs the previous used command (skipping Edit .Undo [z] and File . Open. . . [o] commands). See also: Plugins .Utilities . Reset. . . , Multi Undo plugin 7 Image Types and Formats Digital Images are two-dimensional grids of pixel intensities values with the width and height of the image being defined by the number of pixels in x (rows) and y (columns) direction. Thus, pixels (picture elements) are the smallest single components of images, holding numeric values – pixel intensities – that range between black and white. The characteristics of this range, i.e., the number of unique intensity (brightness) values that can exist in the image is defined as the bit–depth of the image and specifies the level of precision in which intensities are coded, e.g.: A 2–bit image has 2 2 = 4 tones: 00 (black), 01 (gray), 10 (gray), and 11 (white). A 4–bit image has 2 4 = 16 tones ranging from 0000 (0) to 1111 (16), etc. In terms of bits per pixel (bpp), the most frequent types of images (Image .Type . ) that ImageJ deals with are (ImageJ2 supports many more types of image data): 8–bit Images that can display 256 (2 8 ) gray levels (integers only). 16–bit Images that can display 65, 536 (2 16) gray levels (integers only). 32–bit Images that can display 4, 294, 967, 296 (2 32) gray levels (real numbers). In 32–bit images, pixels are described by floating point values and can have any intensity value including NaN (Not a Number). RGB Color Color Images that can display 256 values in the Red, Green and Blue channel. These are 24–bit (2 3×8 ) images. RGB color images can also be 32–bit color images (24–bit color images with additional eight bits coding alpha blending values, i.e., transparency). Native Formats Natively (i.e. without the need of third-party plugins) ImageJ opens the following formats: TIFF, GIF, JPEG, PNG, DICOM, BMP, PGM and FITS. Many more formats are supported with the aid of plugins. These are discussed in Non–native Formats. TIFF (Tagged Image File Format) is the ‘default’ format of ImageJ (cf. File . Save [s]). Images can be 1–bit, 8–bit, 16–bit (unsigned1 ), 32–bit (real) or RGB color. TIFF files with multiple images of the same type and size open as Stacks or Hyperstacks. ImageJ opens lossless compressed TIFF files (see II Image Types: Lossy Compression and Metadata) by the LZW, PackBits and ZIP (Deflate/Inflate) [2] compression schemes. In addition, TIFF files can be opened and saved as ZIP archives. Tiff tags and information needed to import the file (number of images, offset to first images, gap between images) are printed to the Log Window when ImageJ is running in Debug Mode (Edit . Options . Misc. . . , see Settings and Preferences). 1A numeric variable is signed if it can represent both positive and negative numbers, and unsigned if it can only represent positive numbers. 10 Last updated: 2012/10/02