Scientific Imaging Tutorials

<!DOCTYPE html> <html> <head> <title>Scientific Imaging Tutorials</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="Scientific Imaging Tutorials" 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/imaging/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" 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data-toc-headings="h1,h2,h3,h4,h5,h6"></ul> </div> </section>  <div class="container"> <header class="major special"> <h1>Scientific Imaging Tutorials</h1> </header> </div>  <div id="nav-bar"><ul class="shadowed-box"><li>Overview</li><li><a href="/imaging/3d-rendering">3D Rendering</a></li><li><a href="/imaging/annotating-images">Annotating Images</a></li><li><a href="/imaging/chromatic-shift">Chromatic Shift</a></li><li><a href="/imaging/colocalization-acquisition">Colocalization Acquisition</a></li><li><a href="/imaging/colocalization-analysis">Colocalization Analysis</a></li><li><a href="/imaging/color-image-processing">Color Image Processing</a></li><li><a href="/imaging/deconvolution">Deconvolution</a></li><li><a href="/imaging/detect-information-loss">Information Loss</a></li><li><a href="/imaging/image-intensity-processing">Image Intensity Processing</a></li><li><a href="/imaging/particle-analysis">Particle Analysis</a></li><li><a href="/imaging/principles">Principles</a></li><li><a href="/imaging/registration">Registration</a></li><li><a href="/imaging/segmentation">Segmentation</a></li><li><a href="/imaging/spatial-calibration">Spatial Calibration</a></li><li><a href="/imaging/stack-slice-manipulations">Stack‑slice Manipulations</a></li><li><a href="/imaging/t-functions">T‑functions</a></li><li><a href="/imaging/thresholding">Thresholding</a></li><li><a href="/imaging/tracking">Tracking</a></li><li><a href="/imaging/visualization">Visualization</a></li><li><a href="/imaging/voxelization">Voxelization</a></li><li><a href="/imaging/watershed">Watershed Separation</a></li><li><a href="/imaging/z-functions">Z‑functions</a></li></ul></div>  <section id="page" class="main style1"> <div class="container"> <div class="box alt"></div> <div id="content" class="page-content"> <p>This section is an introduction to scientific imaging, including both image acquisition and image analysis, with a focus on ImageJ.</p> <p>Cooks call them <em>recipes</em>, biologists <em>protocols</em>, and programmers call them <em>HOWTOs</em>. No matter how you refer to them, you’ll find all the topics in the nav-bar at the top of the page!</p> <p>Like the rest of this wiki, this guide is a community project. Please feel welcome to <a href="/editing">edit and expand</a> the material here!</p> <div class="notice" style="font-size: 1; background: #e6e6e6; border-left: 10px solid gold"><div class="notice-content"><p>If you are new to scientific imaging, <em>please peruse the <a href="/imaging/principles">Principles</a></em> for a primer!</p> </div> </div> <h2 id="installation">Installation</h2> <p>Some parts of this guide describe plugins from the <a href="/software/fiji">Fiji</a> distribution of ImageJ, as well as from the <a href="/update-sites/cookbook">Cookbook update site</a>. Here’s how to set it up:</p> <style> .cookbook-install-table { width: auto; } .cookbook-install-table img { max-width: 400px; max-height: 200px; } </style> <table class="cookbook-install-table"> <tbody> <tr> <td>1.</td> <td><a href="/software/fiji/downloads">Download and install</a> the Fiji distribution of ImageJ.</td> <td> </td> </tr> <tr> <td>2.</td> <td>From the Fiji menu, select <span class="bc"><span>Help</span> › <span>Update…</span></span></td> <td><img src="/media/imaging/1-update-fiji.png" class="img" alt="1-update-fiji" /></td> </tr> <tr> <td>3.</td> <td>Click <span class="app-button">Manage update sites</span></td> <td><img src="/media/imaging/2-manage-update-sites.png" class="img" alt="2-manage-update-sites" /></td> </tr> <tr> <td>4.</td> <td>Check the <strong>Cookbook</strong> update site</td> <td><img src="/media/imaging/3-enable-cookbook.png" class="img" alt="3-enable-cookbook" /></td> </tr> <tr> <td>5.</td> <td>Click <span class="app-button">Close</span></td> <td> </td> </tr> <tr> <td>6.</td> <td>Click <span class="app-button">Apply changes</span> to download the Cookbook plugins</td> <td><img src="/media/imaging/4-apply-changes.png" class="img" alt="4-apply-changes" /></td> </tr> <tr> <td>7.</td> <td>Restart Fiji to complete the plugin installation</td> <td> </td> </tr> <tr> <td>8.</td> <td>Enjoy your new plugins from the <strong>Cookbook</strong> menu!</td> <td><img src="/media/imaging/5-use-the-cookbook.png" class="img" alt="5-use-the-cookbook" /></td> </tr> </tbody> </table> <h2 id="source">Source</h2> <p>The source code of the Cookbook plugins can be found <a href="https://github.com/fiji/cookbook/">on GitHub</a>.</p> <h2 id="credits">Credits</h2> <p>Many of the pages in this section were adapted from the defunct <a href="/software/mbf-imagej">MBF “ImageJ for microscopy” manual</a>, originally created by Tony Collins, which went offline in November 2012.</p> <p>The Cookbook technical writer team includes:</p> <ul> <li><a class="person" href="/people/ctrueden">Curtis Rueden</a> (technical oversight and maintenance)</li> <li><a class="person" href="/people/apal4">Aparna Pal</a> (January 2014 - May 2015)</li> <li><a class="person" href="/people/dscho">Johannes Schindelin</a> (June 2013 - November 2014)</li> <li><a class="person" href="/people/kghildebrand">Katie Hildebrand</a> (June 2013 - December 2013)</li> <li><a class="person" href="/people/amanda-macallister">Amanda MacAllister</a> (June 2013 - December 2013)</li> <li><a class="person" href="/people/RuizhiLiao">Ruizhi “Ray” Liao</a> (November 2013 - December 2013)</li> <li><a class="person" href="/people/gabby-campagnola">Gabby Campagnola</a> (June 2013 - August 2013)</li> </ul> <p>The plugins featured in the Cookbook were collated from various sources and have various authors and licenses.</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" 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href="/imaging/tracking">Tracking</a></li> <li><a href="/imaging/visualization">Visualization</a></li> <li><a href="/imaging/z-functions">Z-functions</a></li> </ul></details></li>  </ul></details></li>  <li><details><summary><a href="/plugins">Extend</a></summary><ul> <li><a href="/list-of-extensions">List of Extensions</a></li> <li><details><summary><a href="/update-sites">Update Sites</a></summary><ul> <li><a href="/list-of-update-sites">List of Update Sites</a></li> <li><a href="/update-sites/following">Following an Update Site</a></li> <li><a href="/update-sites/setup">Creating an Update Site</a></li> <li><a href="/update-sites/tos">Terms of Service</a></li> <li><a href="/update-sites/automatic-uploads">Automatic Upload</a></li> <li><a href="/update-sites/core-uploads">Uploading to Core Sites</a></li> <li><a href="/update-sites/faq">Update Sites FAQ</a></li> <li><a href="/update-sites/stats">Statistics</a></li> </ul></details></li>  <li><details><summary><a 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href="/scripting/matlab">MATLAB</a></li> <li><a href="/scripting/jython">Python (Jython)</a></li> <li><a href="/scripting/python">Python (native)</a></li> <li><a href="/scripting/renjin">R (Renjin)</a></li> <li><a href="/scripting/jruby">Ruby (JRuby)</a></li> <li><a href="/scripting/scala">Scala Scripting</a></li> </ul></details></li>  </ul></details></li>  <li><details><summary><a href="/develop">Development</a></summary><ul> <li><a href="/develop/philosophy">Philosophy</a></li> <li><a href="/develop/architecture">Architecture</a></li> <li><a href="/develop/source">Source code</a></li> <li><a href="/develop/project-management">Project management</a></li> <li><a href="/develop/coding-style">Coding style</a></li> <li><a href="/develop/javadoc">Using Javadoc</a></li> <li><a href="/develop/debugging">Debugging</a></li> <li><a href="/develop/wish-list">Wish list</a></li> <li><details><summary>Tools</summary><ul> <li><a href="/develop/github">GitHub</a></li> <li><a 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