Introduction

<!DOCTYPE html> <html> <head> <title>Introduction</title> <meta charset="utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=3" /> <meta content="ImageJ Wiki" property="og:site_name"> <meta content="Introduction" property="og:title"> <meta content="article" property="og:type"> <meta content="The ImageJ wiki is a community-edited knowledge base on topics relating to ImageJ, a public domain program for processing and analyzing scientific images, and its ecosystem of derivatives and variants, including ImageJ2, Fiji, and others." property="og:description"> <meta content="https://imagej.github.io/learn/index" property="og:url"> <meta content="https://imagej.github.io/media/icons/imagej2.png" property="og:image"> <link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png"> <link rel="icon" type="image/png" sizes="32x32" href="/favicon-32x32.png"> <link rel="icon" type="image/png" sizes="16x16" href="/favicon-16x16.png"> <link 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</head> <body class="is-preload">  <section id="top-bar"> <a href="/"><img id="site-logo" src="/media/icons/imagej2.png"></a> <div id="search-panel"> <div id="search-box"></div> </div> </section>  <div class="page-info"> <a href="https://github.com/imagej/imagej.github.io/commits/main/_pages/learn/index.md">Page history</a> <a href="https://github.com/imagej/imagej.github.io/edit/main/_pages/learn/index.md">Edit this page</a> <a href="/editing">How do I edit this website?</a></div> <section id="left-column" class="sidebar dock">  <div class="menu dockable"> <div class="drag-handle"></div><h3>ImageJ Docs</h3> <ul> <li><a href="/downloads">Download</a></li> <li><details open><summary>Learn</summary><ul> <li><details open><summary><a class="current-page">ImageJ Basics</a></summary><ul> <li><a href="/tutorials">Tutorials</a></li> <li><a href="/learn/user-guides">User Guides</a></li> <li><a href="/learn/keyboard-shortcuts">Keyboard Shortcuts</a></li> <li><a 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href="/libs/imglib2/workshop-advanced">Advanced Workshop</a></li> <li><a href="/libs/imglib2/matlab">ImgLib2 images in MATLAB</a></li> <li><a href="/libs/imglib2/benchmarks">Benchmarks</a></li> <li><a href="/libs/imglib2/faq">FAQ</a></li> <li><a href="/libs/imglib2/developing">Developing ImgLib2</a></li> <li><a href="/libs/imglib2/discussion">ImgLib2 Discussion</a></li> </ul></details></li>  <li><a href="/libs">More...</a></li> </ul></details></li>  <li><details><summary><a href="/software">Software</a></summary><ul> <li><a href="/software/nih-image">NIH Image</a></li> <li><a href="/software/imagej">ImageJ</a></li> <li><a href="/software/imagej2">ImageJ2</a></li> <li><a href="/software/fiji">Fiji</a></li> <li><a href="/software">More...</a></li> </ul></details></li>  </ul></details></li>  </ul> </div> </section> <section id="right-column" class="sidebar dock">   <div id="toc" class="toc menu dockable"> <div class="drag-handle"></div> <h3>Page contents</h3> <ul data-toc="#content" data-toc-headings="h1,h2,h3,h4,h5,h6"></ul> </div> </section>  <div class="container"> <header class="major special"> <h1>Introduction</h1> </header> </div>  <div id="nav-bar"><ul class="shadowed-box"><li>Introduction</li><li><a href="/learn/faq">FAQ</a></li><li><a href="/learn/headless">Headless</a></li><li><a href="/learn/keyboard-shortcuts">Keyboard Shortcuts</a></li><li><a href="/learn/launcher">Launcher</a></li><li><a href="/learn/tips-and-tricks">Tips and Tricks</a></li><li><a href="/learn/troubleshooting">Troubleshooting</a></li><li><a href="/learn/user-guides">User Guides</a></li></ul></div>  <section id="page" class="main style1"> <div class="container"> <div class="box alt"></div> <div id="content" class="page-content"> <h1 id="what-is-imagej">What is ImageJ?</h1> <p><a href="/software/imagej"><img src="/media/icons/imagej.png" alt="" height="48px" /> ImageJ</a> is <a href="/licensing#a-note-about-imagej">public domain</a> software for processing and analyzing scientific images.</p> <h1 id="what-is-imagej2">What is ImageJ2?</h1> <p><a href="/software/imagej2"><img src="/media/icons/imagej2.png" alt="" height="48px" /> ImageJ2</a> is a new version of ImageJ for multidimensional image data, with a focus on scientific imaging. It includes some additional features not available in the original ImageJ.</p> <h1 id="what-is-fiji">What is Fiji?</h1> <p><a href="/software/fiji"><img src="/media/icons/fiji.svg" alt="" height="48px" /> <span style="color: darkcyan; font-size: large; font-weight: bold">F</span>iji <span style="color: darkcyan; font-size: large; font-weight: bold">I</span>s <span style="color: darkcyan; font-size: large; font-weight: bold">J</span>ust <span style="color: darkcyan; font-size: large; font-weight: bold">I</span>mageJ</a>—a “batteries-included” distribution of ImageJ and ImageJ2 which includes many useful <a href="/plugins">plugins</a> <a href="/contribute/fiji">contributed by the community</a>.</p> <h1 id="what-does-imagej-provide">What does ImageJ provide?</h1> <table> <tbody> <tr> <td><a href="/learn/flavors">Application</a></td> <td>A user interface with functions to load, display, and save images.</td> </tr> <tr> <td><a href="/imaging">Techniques</a></td> <td><a href="/imaging/image-intensity-processing">Image processing</a>, <a href="/imaging/colocalization-analysis">colocalization</a>, <a href="/imaging/deconvolution">deconvolution</a>, <a href="/imaging/registration">registration</a>, <a href="/imaging/segmentation">segmentation</a>, <a href="/imaging/tracking">tracking</a>, <a href="/imaging/visualization">visualization</a> and much more.</td> </tr> <tr> <td><a href="/plugins">Plugins</a></td> <td>A powerful mechanism for extending ImageJ in all kinds of useful ways.</td> </tr> <tr> <td><a href="/scripting">Scripting</a></td> <td>Automated, reproducible workflows via <a href="/scripting">scripts</a> and <a href="/scripting/macro">macros</a>.</td> </tr> <tr> <td><a href="https://forum.image.sc/tag/imagej">Forum</a></td> <td>A vibrant, diverse, and helpful user <a href="/discuss">community</a>.</td> </tr> </tbody> </table> <p>ImageJ’s <a href="/develop/architecture#extensibility">extensibility</a> is the root of its effectiveness: many advanced image-processing methods are not provided by the core application, but rather are <a href="/plugins">plugins</a> written by specialists in specific fields, made available via <a href="/update-sites">ImageJ2 update sites</a>.</p> <h1 id="how-do-i-get-started">How do I get started?</h1> <h2 id="installation">Installation</h2> <p>First, you should <a href="/downloads">download</a> and install ImageJ, ImageJ2, or Fiji!</p> <h2 id="the-main-window">The main window</h2> <p>After starting the program, you will see the main window:</p> <p><img src="/media/learn/fiji-main-window.png" alt="fiji-main-window" width="700px" /></p> <p>On macOS, the menu bar will appear on the top of the screen (as with all macOS applications).</p> <h3 id="the-search-bar">The search bar</h3> <div class="notice" style="font-size: 2; background: #e6e6e6; border-left: 10px solid goldenrod"><div class="notice-icon"><img src="/media/icons/imagej.png" /></div><div class="notice-content"> <p>The original version of ImageJ does not have a search bar, but you can bring up the Command Finder, with some similar capabilities, by pressing the same keyboard shortcut: <span class="tooltip" style="padding-bottom: 4px"><kbd class="key">⌃ Ctrl / ⌘</kbd><span class="tooltiptext" style="top: 80%; left: 25%; width: 20em"><span class="ctlcmd"> <span><kbd class="key">⌃ Ctrl</kbd></span> <span>on a PC</span> <span><kbd class="key">⌘ command</kbd></span> <span>on a Mac</span> </span></span></span> + <kbd class="key">L</kbd></p> </div> </div> <p>The search bar is a convenient way to quickly find and launch commands, search for documentation, and more. The search panel can be brought up by clicking and typing into the search bar, or via the keyboard shortcut <span class="tooltip" style="padding-bottom: 4px"><kbd class="key">⌃ Ctrl / ⌘</kbd><span class="tooltiptext" style="top: 80%; left: 25%; width: 20em"><span class="ctlcmd"> <span><kbd class="key">⌃ Ctrl</kbd></span> <span>on a PC</span> <span><kbd class="key">⌘ command</kbd></span> <span>on a Mac</span> </span></span></span> + <kbd class="key">L</kbd></p> <p><img src="/media/learn/fiji-search-window.png" alt="fiji-search-window" width="700px" /></p> <p><strong>Results</strong></p> <p>These are the plugins/commands that match your search query, sorted by type of result. Results can be navigated with the mouse or arrow keys, and the highlighted command can be executed with <kbd class="key">&crarr; Enter</kbd> or double-clicking.</p> <p><strong>Categories</strong></p> <p>Categories can be (de)selected as desired to expand or restrict the scope of your search, as desired.</p> <p><strong>Search Options</strong></p> <p><img src="/media/learn/fiji-search-options.png" alt="fiji-search-options" width="400px" /></p> <p>The <code class="language-plaintext highlighter-rouge">...</code> button opens a panel with more options for controlling your search behavior.</p> <p><strong>Details</strong></p> <p>The details panel provides more information about the selected search result.</p> <p><strong>Action Buttons</strong></p> <p>These buttons can be used to take alternative actions (beyond just running a given command) such as opening the plugin’s source or wiki page.</p> <h3 id="the-menu-bar">The menu bar</h3> <p>In the menu bar, you will find most of the functionality, such as loading/saving files, processing them, and plugins will be installed into the menus, too.</p> <p>The menus have different purposes:</p> <table> <tbody> <tr> <td>File</td> <td>File input/output, new files</td> </tr> <tr> <td>Edit</td> <td>Selection/ROI handling</td> </tr> <tr> <td>Image</td> <td>Visualization, stack manipulation</td> </tr> <tr> <td>Process</td> <td>Image filters</td> </tr> <tr> <td>Analyze</td> <td>Statistics</td> </tr> <tr> <td>Plugins</td> <td>Plugins, Macros and Utilities</td> </tr> <tr> <td>Window</td> <td>Windows</td> </tr> <tr> <td>Help</td> <td>Help & Links</td> </tr> </tbody> </table> <h3 id="the-tool-bar">The tool bar</h3> <p>The toolbar mostly contains selection tools: the rectangle, ellipse, polygon, freehand and straight line selection tool. By clicking on the icon, you activate the tool.</p> <p>Some tools offer option dialogs which you can open by double clicking the icon. This example shows the option dialog of the Oval Tool:</p> <p><img src="/media/learn/oval-tool-option-dialog.png" alt="" /></p> <p>If there is a small red arrow in the lower right corner of the tool icon, you can right-click (<kbd class="key">⌃ Ctrl</kbd> + <span class="key"><img src="https://upload.wikimedia.org/wikipedia/commons/2/27/LMB_click.svg" /> Left Click</span> on an Apple mouse) and select an alternative selection tool (e.g. a circular brush selection tool which shares the icon with the ellipse selection tool). Example:</p> <p><img src="/media/learn/alternative-tools.png" alt="" /></p> <h3 id="the-status-bar">The status bar</h3> <p>The status bar displays useful information at startup, and when running plugins. It also shows a progress bar on the right side for long-running processes:</p> <p><img src="/media/learn/status-bar-with-progress.png" alt="" /></p> <p>A single mouse click on the status bar will show the information about ImageJ and Java version as well as about memory consumption:</p> <p><img src="/media/learn/default-status-message.png" alt="" /></p> <h3 id="drag--drop">Drag & Drop</h3> <p>You can drag files from your favorite file manager and drop them on the main window; ImageJ will load the corresponding files.</p> <p>Drag ‘n Drop will also work for images displayed in your web browser, unless they are links to other web pages. You can try with images from this page.</p> <h2 id="image-windows">Image windows</h2> <p>Whenever you open an image, be it via <span class="bc"><span>File</span> › <span>Open</span></span>, Drag ‘n Drop or <span class="bc"><span>File</span> › <span>Open Samples</span></span>, ImageJ will open an image window.</p> <p><img src="/media/learn/clown-snapshot.jpg" alt="" /></p> <p>The window has the file name as title, and it display some useful information above the image: the real resolution (in this case in square centimeters), the pixel resolution, the image type and the memory required by the image.</p> <p>If your image does not have meta-data about the real resolution, you can set the resolution explicitely with <span class="bc"><span>Image</span> › <span>Properties…</span></span> or by following the <a href="/imaging/spatial-calibration">tutorial on spatial calibration</a>.</p> <h3 id="image-types">Image Types</h3> <p>You can change the image <em>type</em>:</p> <p><img src="/media/image-types.png" alt="" /></p> <p>Choose between</p> <ul> <li>8-bit (intensity range 0..255)</li> <li>16-bit (intensity range 0..65535)</li> <li>32-bit (floating point numbers)</li> <li>8-bit color (up to 256 colors encoded via a color lookup table)</li> <li>RGB color (3 colors encoded as 8-bit values)</li> </ul> <p>There are two more options: RGB stack and HSV stack, which can turn a 2-dimensional color image into a stack consisting of 3 color channels (red, green & blue or hue, saturation & value, respectively).</p> <h2 id="further-reading">Further reading</h2> <p>Peruse the <a href="/learn/user-guides">user guides</a>, additional <a href="/tutorials">tutorials</a>, and <a href="/events/presentations">presentations</a>.</p> </div> </div> </section>  <section id="footer"> <ul class="icons"> <li><a href="https://forum.image.sc/tag/imagej" class="icon alt"><img src="/media/icons/image-sc.png" width="24" style="vertical-align: middle; margin-top: -10px"><span 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