FIBSEM importer

<!DOCTYPE html> <html> <head> <title>FIBSEM importer</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="FIBSEM importer" 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/formats/fib-sem" property="og:url"> <meta content="https://imagej.github.io/media/icons/imagej2.png" property="og:image"> <meta content="Import-Export" property="article:section"> <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 rel="manifest" href="/site.webmanifest"> <link rel="mask-icon" href="/safari-pinned-tab.svg" color="#5bbad5"> <meta name="msapplication-TileColor" content="#da532c"> <meta name="theme-color" content="#ffffff"> <link rel="stylesheet" href="/assets/css/lightbox.min.css" /> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/instantsearch.css@7/themes/algolia-min.css"/> <script type="text/javascript" src="https://cdn.jsdelivr.net/npm/dygraphs@2.1.0/dist/dygraph.min.js"></script> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/dygraphs@2.1.0/dist/dygraph.min.css" /> <link rel="stylesheet" href="/assets/css/main.css" /> <link rel="stylesheet" href="/assets/css/layout.css"/> <link rel="stylesheet" href="/assets/css/includes.css" /> <link rel="stylesheet" href="/assets/css/timeline.css"/> <link rel="stylesheet" href="/assets/css/dock.css"/> <noscript><link rel="stylesheet" href="/assets/css/noscript.css" /></noscript> <link rel="stylesheet" href="/assets/css/page.css" /> </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/formats/fib-sem.md">Page history</a> <a href="https://github.com/imagej/imagej.github.io/edit/main/_pages/formats/fib-sem.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 href="/learn">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 href="/learn/tips-and-tricks">Tips and Tricks</a></li> <li><a href="/learn/troubleshooting">Troubleshooting</a></li> <li><a href="/learn/faq">Frequently Asked Questions</a></li> <li><details><summary><a href="/platforms">Supported Platforms</a></summary><ul> <li><a href="/platforms/windows">Windows</a></li> <li><a href="/platforms/macos">MacOS</a></li> <li><a href="/platforms/linux">Linux</a></li> <li><a href="/platforms/pi">Raspberry Pi</a></li> <li><a href="/platforms/android">Android</a></li> </ul></details></li>  <li><details open><summary><a href="/formats">File Formats</a></summary><ul> <li><a href="/formats/bio-formats">Bio-Formats</a></li> <li><a href="/formats/video">Video formats</a></li> <li><a href="/formats/quicktime">QuickTime</a></li> <li><a href="/formats/tiff">TIFF</a></li> <li><a href="/formats/pdf">PDF</a></li> <li><a href="/formats/dicom">DICOM</a></li> <li><a href="/formats/lsm">Zeiss LSM</a></li> <li><a href="/formats/olympus">Olympus VSI</a></li> <li><a href="/formats/lurawave">Opera Flex</a></li> <li><a class="current-page">FIB-SEM</a></li> </ul></details></li>  </ul></details></li>  <li><details><summary><a href="/imaging">Scientific Imaging</a></summary><ul> <li><a href="/imaging/principles">Principles of Scientific Imaging</a></li> <li><a href="/imaging/annotating-images">Annotating Images</a></li> <li><a href="/imaging/colocalization-analysis">Colocalization</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/image-intensity-processing">Image Intensity Processing</a></li> <li><a href="/imaging/particle-analysis">Particle Analysis</a></li> <li><a href="/imaging/registration">Registration</a></li> <li><a href="/imaging/segmentation">Segmentation</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/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 href="/scripting">Scripting</a></summary><ul> <li><a href="/scripting/basics">Scripting Basics</a></li> <li><a href="/scripting/script-editor">Script Editor</a></li> <li><a href="/scripting/parameters">Parameters</a></li> <li><a href="/scripting/user-input">User Input</a></li> <li><a href="/scripting/auto-imports">Auto Import</a></li> <li><a href="/scripting/templates">Templates</a></li> <li><a href="/scripting/batch">Batch Processing</a></li> <li><a href="/scripting/headless">Running Headlessly</a></li> <li><a href="/scripting/comparisons">Scripting Comparisons</a></li> <li><a href="/scripting/toolbox">Toolbox</a></li> <li><details><summary>Languages</summary><ul> <li><a href="/scripting/beanshell">BeanShell Scripting</a></li> <li><a href="/scripting/groovy">Groovy Scripting</a></li> <li><a href="/scripting/macro">ImageJ Macro</a></li> <li><a href="/scripting/javascript">JavaScript</a></li> <li><a href="/scripting/clojure">Lisp (Clojure)</a></li> <li><a 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 href="/develop/maven">Maven</a></li> <li><a href="/develop/ci">CI/CD</a></li> <li><a href="/develop/dotfiles">Dotfiles</a></li> <li><details><summary><a href="/develop/ides">IDEs</a></summary><ul> <li><a href="/develop/eclipse">Eclipse</a></li> <li><a href="/develop/netbeans">NetBeans</a></li> <li><a href="/develop/intellij">IntelliJ IDEA</a></li> <li><a href="/develop/command-line">Command Line</a></li> </ul></details></li> </ul></details></li>  <li><details><summary>Guides</summary><ul> <li><a href="/develop/plugins">Writing plugins</a></li> <li><a href="/develop/improving-the-code">Contributing to a plugin</a></li> <li><a href="/develop/releasing">Development lifecycle</a></li> <li><a href="/develop/building-a-pom">Building a POM</a></li> <li><a href="/develop/debugging-exercises">Hands-on debugging</a></li> <li><a href="/develop/writing-ops">Adding new ops</a></li> <li><a href="/develop/formats">Adding new formats</a></li> <li><a href="/develop/native-libraries">Using native libraries</a></li> <li><a href="/develop/tips">Tips for developers</a></li> <li><a href="/develop/cpp-tips">Tips for C++ developers</a></li> <li><a href="/develop/ij1-plugins">ImageJ 1.x plugins</a></li> <li><a href="/develop/versioning">Versioning</a></li> <li><a href="/develop/logging">Logging</a></li> <li><a href="/develop/uber-jars">Uber-JARs</a></li> </ul></details></li>  <li><details><summary><a href="/develop/git">Git</a></summary><ul> <li><a href="/develop/git/eclipse">Git in Eclipse (EGit)</a></li> <li><a href="/develop/git/mini-howto">Git mini howto</a></li> <li><a href="/develop/git/workshop">Git workshop</a></li> <li><a href="/develop/git/conflicts">Git conflicts</a></li> <li><a href="/develop/git/topic-branches">Git topic branches</a></li> <li><a href="/develop/git/notes">Git notes</a></li> <li><a href="/develop/git/reflogs">Git reflogs</a></li> <li><a href="/develop/git/submodules">Git submodules</a></li> <li><a href="/develop/git/pinpoint-regressions">How to pinpoint regressions</a></li> <li><a href="/develop/git/publish-a-repository">How to publish a git repository</a></li> <li><a href="/develop/git/extract-a-subproject">How to extract a subproject</a></li> </ul></details></li>  </ul></details></li>  </ul></details></li>  <li><details><summary><a href="/contribute">Contribute</a></summary><ul> <li><a href="/contribute/citing">Citing</a></li> <li><a href="/people">Contributors</a></li> <li><a href="/orgs">Organizations</a></li> <li><a href="/contribute/governance">Governance</a></li> <li><a href="/contribute/funding">Funding</a></li> <li><a href="/contribute/fiji">Contributing to Fiji</a></li> <li><details><summary><a href="/licensing">Licensing</a></summary><ul> <li><details><summary><a href="/licensing/open-source">Open Source</a></summary><ul> <li><a href="/licensing/apache">Apache</a></li> <li><a href="/licensing/bsd">BSD</a></li> <li><a href="/licensing/epl">EPL</a></li> <li><a href="/licensing/gpl">GPL</a></li> <li><a href="/licensing/lgpl">LGPL</a></li> <li><a href="/licensing/mit">MIT</a></li> <li><a href="/licensing/public-domain">Public domain</a></li> <li><a href="/licensing/big">BIG</a></li> </ul></details></li>  <li><a href="/licensing/closed-source">Proprietary</a></li> </ul></details></li>  <li><details><summary><a href="/editing">Editing the Wiki</a></summary><ul> <li><a href="/editing/advanced">Advanced Editing</a></li> <li><a href="/editing/buttons">Buttons</a></li> <li><a href="/editing/citations">Citations</a></li> <li><a href="/editing/code">Source Code</a></li> <li><a href="/editing/debugging">Debugging</a></li> <li><a href="/editing/headers">Headers</a></li> <li><a href="/editing/icons">Icons</a></li> <li><a href="/editing/images">Images</a></li> <li><a href="/editing/keys">Keyboard Shortcuts</a></li> <li><a href="/editing/linking">Linking</a></li> <li><a href="/editing/math">Math Expressions</a></li> <li><a href="/editing/menu-paths">Menu Paths</a></li> <li><a href="/editing/navigation">Navigation</a></li> <li><a href="/editing/notices">Notices</a></li> <li><a href="/editing/people">People</a></li> <li><a href="/editing/pitfalls">Pitfalls</a></li> <li><a href="/editing/quizzes">Quizzes</a></li> <li><a href="/editing/statbox">Statbox</a></li> <li><a href="/editing/symbols">Symbols</a></li> <li><a href="/editing/tables">Tables</a></li> <li><a href="/editing/timelines">Timelines</a></li> <li><a href="/editing/tooltips">Tooltips</a></li> <li><a href="/editing/videos">Videos</a></li> <li><a href="/editing/whitespace">Whitespace</a></li> </ul></details></li>  </ul></details></li>  <li><details><summary><a href="/discuss">Discuss</a></summary><ul> <li><a href="/discuss/bugs">Reporting Issues</a></li> <li><a href="/discuss/mailing-lists">Mailing Lists</a></li> <li><a href="/discuss/chat">Chat</a></li> </ul></details></li>  <li><details><summary>Explore</summary><ul> <li><a href="/news">News</a></li> <li><details><summary><a href="/events">Events</a></summary><ul> <li><a href="/events/presentations">Presentations</a></li> <li><a href="/events/conferences">Conferences</a></li> <li><a href="/events/hackathons">Hackathons</a></li> <li><a href="/events">More...</a></li> </ul></details></li>  <li><details><summary><a href="/libs">Libraries</a></summary><ul> <li><a href="/libs/imagej-ops">ImageJ Ops</a></li> <li><a href="/libs/imagej-common">ImageJ Common</a></li> <li><a href="/libs/imagej-legacy">ImageJ Legacy</a></li> <li><a href="/libs/scijava">SciJava</a></li> <li><a href="/libs/scifio">SCIFIO</a></li> <li><details><summary><a href="/libs/imglib2">ImgLib2</a></summary><ul> <li><a href="/libs/imglib2/getting-started">Getting Started</a></li> <li><a href="/libs/imglib2/accessors">Accessors</a></li> <li><a href="/libs/imglib2/accessibles">Accessibles</a></li> <li><a href="/libs/imglib2/examples">Examples</a></li> <li><a href="/libs/imglib2/workshop-introductory">Introductory Workshop</a></li> <li><a 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">  <script src="/assets/js/maven.js"></script> <script> function refreshComponent() { var statboxName = document.getElementById('statbox-name'); if (statboxName) statboxName.innerHTML = 'Reloading...'; fillStatsFromArtifact('sc.fiji:IO_', ''); } refreshComponent(); </script><div id="statbox" class="dockable" style="position: relative;"> <h3>Vital statistics</h3> <div class="drag-handle"></div> <button class="btn-refresh" onclick="refreshComponent()"><i class="fa fa-sync" style="pointer-events: none;"></i></button> <table><tr><td id="statbox-header" colspan=2><p id="statbox-image"><img src="/media/icons/plugin.png"></p> <p id="statbox-name">FIBSEM importer</p></td></tr><tr><th>Source</th> <td id="component-source">none</td></tr><tr><th>License</th> <td id="component-license"></td></tr><tr><th>Release</th> <td id="component-release"></td></tr><tr><th>Date</th> <td id="component-date"></td></tr><tr><th>Development status</th> <td id="component-dev-status"></td></tr><tr><th>Support status</th> <td id="component-support-status"></td></tr><tr><td id="component-team" colspan=2> <details> <summary style="text-align: center"><span class="tooltip">Team<span class="tooltiptext" style="top: 80%; left: -75px; width: 180px">The group of people who take responsibility for the project.</span></span></summary> <table><tr><th><span class="tooltip">Founders<span class="tooltiptext" style="top: 80%; left: -10px; width: 180px">People who created the project. Does not imply any current participation or responsibility.</span></span></th><td id="component-team-founders"></td> </tr><tr><th><span class="tooltip">Leads<span class="tooltiptext" style="top: 80%; left: -10px; width: 180px">People responsible for making decisions about the project: timing of releases, inclusion of features, etc.</span></span></th><td id="component-team-leads"></td> </tr><tr><th><span class="tooltip">Developers<span class="tooltiptext" style="top: 80%; left: -10px; width: 180px">People responsible for adding new features or enhancements.</span></span></th><td id="component-team-developers"></td> </tr><tr><th><span class="tooltip">Debuggers<span class="tooltiptext" style="top: 80%; left: -10px; width: 180px">People responsible for fixing bugs.</span></span></th><td id="component-team-debuggers"></td> </tr><tr><th><span class="tooltip">Reviewers<span class="tooltiptext" style="top: 80%; left: -10px; width: 180px">People responsible for reviewing patch submissions.</span></span></th><td id="component-team-reviewers"></td> </tr><tr><th><span class="tooltip">Support<span class="tooltiptext" style="top: 80%; left: -10px; width: 180px">People responsible for responding to community questions and issue reports.</span></span></th><td id="component-team-support"></td> </tr><tr><th><span class="tooltip">Maintainers<span class="tooltiptext" style="top: 80%; left: -10px; width: 180px">People responsible for maintaining the project: e.g., merging patch submissions and cutting releases.</span></span></th><td id="component-team-maintainers"></td> </tr><tr><th><span class="tooltip">Contributors<span class="tooltiptext" style="top: 80%; left: -10px; width: 180px">People who contributed code to the project. Does not imply any current participation or responsibility.</span></span></th><td id="component-team-contributors"></td> </tr></table> </details> </td></tr></table> </div>  <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>FIBSEM importer</h1> </header> </div>  <div id="nav-bar"><ul class="shadowed-box"><li><a href="/formats/index">Formats</a></li><li><a href="/formats/animated-gif">Save as animated gif</a></li><li><a href="/formats/bio-formats">Bio‑Formats</a></li><li><a href="/formats/dicom">DICOM</a></li><li>FIBSEM importer</li><li><a href="/formats/lsm">LSM Toolbox</a></li><li><a href="/formats/lurawave">LuraWave</a></li><li><a href="/formats/metadata">Metadata</a></li><li><a href="/formats/olympus">OlympusImageJPlugin</a></li><li><a href="/formats/pdf">Extract Images From PDF...</a></li><li><a href="/formats/quicktime">QuickTime</a></li><li><a href="/formats/tia-ser-folder-export">TIA .ser folder export</a></li><li><a href="/formats/tiff">TIFF</a></li><li><a href="/formats/vaa3d-reader">Vaa3d Reader</a></li><li><a href="/formats/vaa3d-writer">Vaa3d Writer</a></li><li><a href="/formats/video">Video</a></li><li><a href="/formats/wavefront-obj">Wavefront .OBJ ...</a></li></ul></div>  <section id="page" class="main style1"> <div class="container"> <div class="box alt"></div> <div id="content" class="page-content"> <h2 id="overview">Overview</h2> <p>The FIBSEM importer is able to read the image files produced by the FIB-SEM machine at Janelia Farm. It can be used via:</p> <ul> <li>Drag & Drop</li> <li><span class="bc"><span>File</span> › <span>Import</span> › <span>FIB-SEM …</span></span></li> </ul> <p>It will be opened as unsigned 16-bit data ranging from 0 to 65535, where 0 corresponds to a detector voltage of -10 volts and 65535 to a voltage of +10 volts. It will automatically set the pixel resolution in the image calibration.</p> <p>For access to all the other meta-data, see the special options paragraph below.</p> <h2 id="special-options">Special options</h2> <h3 id="open-image-as-float">Open image as float</h3> <p>It might make sense to open the image as float and not convert it into an unsigned short. To do so, one can set a switch in the FIBSEM importer using the <strong>script editor</strong>:</p> <ul> <li><span class="bc"><span>File</span> › <span>New</span> › <span>Script</span></span></li> <li><span class="bc"><span>Language</span> › <span>Beanshell</span></span></li> <li>type the following lines</li> </ul> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>import io.FIBSEM_Reader; FIBSEM_Reader.openAsFloat = true; </code></pre></div></div> <ul> <li>click Run</li> </ul> <p>From now on, every FIBSEM image of the <strong>currently running Fiji instance</strong> will be opened as float, the float values represent directly the measured voltage for each pixel.</p> <h3 id="access-the-complete-metadata">Access the complete metadata</h3> <p>In order to access the complete metadata you have to make a new instance of the FIBSEM importer, load the dataset and afterwards request the metadata object. Here is the code how do it using the script editor and the Beanshell language (see above):</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>import io.FIBSEM_Reader; import io.FIBSEM_Reader.FIBSEMData; // open the file FIBSEM_Reader reader = new FIBSEM_Reader(); reader.run( "/Users/preibischs/Desktop/Zeiss_12-01-14_210123.dat" ); // get the metadata FIBSEMData metadata = reader.getHeader(); // print all data into the log window IJ.log( "" + metadata ); // print a single field IJ.log( "The resolution of the image is " + metadata.xRes + " x " + metadata.yRes + " pixels." ); </code></pre></div></div> <p>Below you will find a complete list of all fields of <strong>FIBSEMData</strong>, i.e. all metadata information that you can access:</p> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>/* the magic number identifying the file, should be 3555587570 */ public long magicNumber; /* the version of the file, supported until now is 1,2,3 */ public int fileVersion; /* file type, 1 is Zeiss Neon detectors */ public int fileType; /* AI sampling time (including oversampling) in seconds */ public double timeStep; /* the number of channels */ public int numChannels; /* the parameters required to transform the 16 bit signed signal back to volts: * volts = offset + intensity*gain * (we ignore second and third order as they are zero anyways) */ public float[] offset, gain, secondOrder, thirdOrder; /* number of pixels in x per channel */ public long xRes; /* number of pixels in y per channel */ public long yRes; /* AI oversampling */ public int oversampling; /* Read AI delay (# of samples) - only v3*/ public int AIdelay = 0; /* Scan speed (Zeiss #) */ public int zeissScanSpeed; /* Actual AO (scanning) rate */ public double scanRate; /* Frameline rampdown ratio */ public double framelineRampdownRatio; /* X coil minimum voltage */ public double xMin; /* X coil maximum voltage */ public double xMax; /* Detector minimum voltage */ public double detMin; /* Detector maximum voltage */ public double detMax; /* AI Ch1 */ public int AI1; /* AI Ch2 */ public int AI2; /* AI Ch3 */ public int AI3; /* AI Ch4 */ public int AI4; /* notes */ public String notes; /* Name of detector A */ public String detectorA = ""; /* Name of detector B */ public String detectorB = ""; /* Name of detector C */ public String detectorC = ""; /* Name of detector D */ public String detectorD = ""; /* Magnification */ public double magnification; /* Pixel size in nm */ public double pixelSize; /* Working distance in mm */ public double wd; /* EHT in kV */ public double eht; /* SEM aperture number */ public int semApr; /* high current mode (1=on, 0=off) */ public int highCurrent; /* FIB mode: 0=SEM, 1=FIB, 2=Milling, 3=SEM+FIB, 4=Mill+SEM, 5=SEM Drift Correction, 6=FIB Drift Correction, 7=No Beam, 8=External, 9=External+SEM */ public int mode; /* SEM probe current in A */ public double semCurr; /* SEM scan roation in degree */ public double semRot; /* Chamber Vacuum */ public double chamVac; /* Gun vacuum */ public double gunVac; /* SEM beam shift X */ public double semShiftX; /* SEM beam shift Y */ public double semShiftY; /* SEM stigmation X */ public double semStiX; /* SEM stigmation Y */ public double semStiY; /* SEM aperture alignment X */ public double semAlnX; /* SEM aperture alignment Y */ public double semAlnY; /* Stage position X in mm */ public double stageX; /* Stage position Y in mm */ public double stageY; /* Stage position Z in mm */ public double stageZ; /* Stage position T in degree */ public double stageT; /* Stage position R in degree */ public double stageR; /* Stage position M in mm */ public double stageM; /* Detector A brightness (%) */ public double brightnessA; /* Detector A contrast (%) */ public double contrastA; /* Detector B brightness (%) */ public double brightnessB; /* Detector B contrast (%) */ public double contrastB; /* FIB focus in kV */ public double fibFocus; /* FIB probe number */ public int fibProb; /* FIB emission current */ public double fibCurr; /* FIB scan rotation */ public double fibRot; /* FIB aperture alignment X */ public double fibAlnX; /* FIB aperture alignment Y */ public double fibAlnY; /* FIB stigmation X */ public double fibStiX; /* FIB stigmation Y */ public double fibStiY; /* FIB beam shift X in micron */ public double fibShiftX; /* FIB beam shift Y in micron */ public double fibShiftY; /* name of the machine */ public String machineID; /* file length in bytes */ public long fileLength; </code></pre></div></div> </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 class="label">Forum</span></a></li> <li><a href="https://twitter.com/hashtag/ImageJ" class="icon brands alt fa-twitter"><span class="label">Twitter</span></a></li> <li><a href="https://github.com/imagej" class="icon brands alt fa-github"><span class="label">GitHub</span></a></li> </ul> <ul class="copyright"> <li>Design: <a href="http://html5up.net">HTML5 UP</a></li> </ul> </section>  <nav role="navigation"> <div id="ham-toggle"> <input type="checkbox" /> <span></span>  <span></span>  <span></span>  <ul id="ham-menu"> <div class="menu"><h3>ImageJ Docs</h3> <ul> <li><a href="/downloads">Download</a></li> <li><details open><summary>Learn</summary><ul> <li><details open><summary><a href="/learn">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 href="/learn/tips-and-tricks">Tips and Tricks</a></li> <li><a href="/learn/troubleshooting">Troubleshooting</a></li> <li><a href="/learn/faq">Frequently Asked Questions</a></li> <li><details><summary><a href="/platforms">Supported Platforms</a></summary><ul> <li><a href="/platforms/windows">Windows</a></li> <li><a href="/platforms/macos">MacOS</a></li> <li><a href="/platforms/linux">Linux</a></li> <li><a href="/platforms/pi">Raspberry Pi</a></li> <li><a href="/platforms/android">Android</a></li> </ul></details></li>  <li><details open><summary><a href="/formats">File Formats</a></summary><ul> <li><a href="/formats/bio-formats">Bio-Formats</a></li> <li><a href="/formats/video">Video formats</a></li> <li><a href="/formats/quicktime">QuickTime</a></li> <li><a href="/formats/tiff">TIFF</a></li> <li><a href="/formats/pdf">PDF</a></li> <li><a href="/formats/dicom">DICOM</a></li> <li><a href="/formats/lsm">Zeiss LSM</a></li> <li><a href="/formats/olympus">Olympus VSI</a></li> <li><a href="/formats/lurawave">Opera Flex</a></li> <li><a class="current-page">FIB-SEM</a></li> </ul></details></li>  </ul></details></li>  <li><details><summary><a href="/imaging">Scientific Imaging</a></summary><ul> <li><a href="/imaging/principles">Principles of Scientific Imaging</a></li> <li><a href="/imaging/annotating-images">Annotating Images</a></li> <li><a href="/imaging/colocalization-analysis">Colocalization</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/image-intensity-processing">Image Intensity Processing</a></li> <li><a href="/imaging/particle-analysis">Particle Analysis</a></li> <li><a href="/imaging/registration">Registration</a></li> <li><a href="/imaging/segmentation">Segmentation</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/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 href="/scripting">Scripting</a></summary><ul> <li><a href="/scripting/basics">Scripting Basics</a></li> <li><a href="/scripting/script-editor">Script Editor</a></li> <li><a href="/scripting/parameters">Parameters</a></li> <li><a href="/scripting/user-input">User Input</a></li> <li><a href="/scripting/auto-imports">Auto Import</a></li> <li><a href="/scripting/templates">Templates</a></li> <li><a href="/scripting/batch">Batch Processing</a></li> <li><a href="/scripting/headless">Running Headlessly</a></li> <li><a href="/scripting/comparisons">Scripting Comparisons</a></li> <li><a href="/scripting/toolbox">Toolbox</a></li> <li><details><summary>Languages</summary><ul> <li><a href="/scripting/beanshell">BeanShell Scripting</a></li> <li><a href="/scripting/groovy">Groovy Scripting</a></li> <li><a href="/scripting/macro">ImageJ Macro</a></li> <li><a href="/scripting/javascript">JavaScript</a></li> <li><a href="/scripting/clojure">Lisp (Clojure)</a></li> <li><a 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 href="/develop/maven">Maven</a></li> <li><a href="/develop/ci">CI/CD</a></li> <li><a href="/develop/dotfiles">Dotfiles</a></li> <li><details><summary><a href="/develop/ides">IDEs</a></summary><ul> <li><a href="/develop/eclipse">Eclipse</a></li> <li><a href="/develop/netbeans">NetBeans</a></li> <li><a href="/develop/intellij">IntelliJ IDEA</a></li> <li><a href="/develop/command-line">Command Line</a></li> </ul></details></li> </ul></details></li>  <li><details><summary>Guides</summary><ul> <li><a href="/develop/plugins">Writing plugins</a></li> <li><a href="/develop/improving-the-code">Contributing to a plugin</a></li> <li><a href="/develop/releasing">Development lifecycle</a></li> <li><a href="/develop/building-a-pom">Building a POM</a></li> <li><a href="/develop/debugging-exercises">Hands-on debugging</a></li> <li><a href="/develop/writing-ops">Adding new ops</a></li> <li><a href="/develop/formats">Adding new formats</a></li> <li><a href="/develop/native-libraries">Using native libraries</a></li> <li><a href="/develop/tips">Tips for developers</a></li> <li><a href="/develop/cpp-tips">Tips for C++ developers</a></li> <li><a href="/develop/ij1-plugins">ImageJ 1.x plugins</a></li> <li><a href="/develop/versioning">Versioning</a></li> <li><a href="/develop/logging">Logging</a></li> <li><a href="/develop/uber-jars">Uber-JARs</a></li> </ul></details></li>  <li><details><summary><a href="/develop/git">Git</a></summary><ul> <li><a href="/develop/git/eclipse">Git in Eclipse (EGit)</a></li> <li><a href="/develop/git/mini-howto">Git mini howto</a></li> <li><a href="/develop/git/workshop">Git workshop</a></li> <li><a href="/develop/git/conflicts">Git conflicts</a></li> <li><a href="/develop/git/topic-branches">Git topic branches</a></li> <li><a href="/develop/git/notes">Git notes</a></li> <li><a href="/develop/git/reflogs">Git reflogs</a></li> <li><a href="/develop/git/submodules">Git submodules</a></li> <li><a href="/develop/git/pinpoint-regressions">How to pinpoint regressions</a></li> <li><a href="/develop/git/publish-a-repository">How to publish a git repository</a></li> <li><a href="/develop/git/extract-a-subproject">How to extract a subproject</a></li> </ul></details></li>  </ul></details></li>  </ul></details></li>  <li><details><summary><a href="/contribute">Contribute</a></summary><ul> <li><a href="/contribute/citing">Citing</a></li> <li><a href="/people">Contributors</a></li> <li><a href="/orgs">Organizations</a></li> <li><a href="/contribute/governance">Governance</a></li> <li><a href="/contribute/funding">Funding</a></li> <li><a href="/contribute/fiji">Contributing to Fiji</a></li> <li><details><summary><a href="/licensing">Licensing</a></summary><ul> <li><details><summary><a href="/licensing/open-source">Open Source</a></summary><ul> <li><a href="/licensing/apache">Apache</a></li> <li><a href="/licensing/bsd">BSD</a></li> <li><a href="/licensing/epl">EPL</a></li> <li><a href="/licensing/gpl">GPL</a></li> <li><a href="/licensing/lgpl">LGPL</a></li> <li><a href="/licensing/mit">MIT</a></li> <li><a href="/licensing/public-domain">Public domain</a></li> <li><a href="/licensing/big">BIG</a></li> </ul></details></li>  <li><a href="/licensing/closed-source">Proprietary</a></li> </ul></details></li>  <li><details><summary><a href="/editing">Editing the Wiki</a></summary><ul> <li><a href="/editing/advanced">Advanced Editing</a></li> <li><a href="/editing/buttons">Buttons</a></li> <li><a href="/editing/citations">Citations</a></li> <li><a href="/editing/code">Source Code</a></li> <li><a href="/editing/debugging">Debugging</a></li> <li><a href="/editing/headers">Headers</a></li> <li><a href="/editing/icons">Icons</a></li> <li><a href="/editing/images">Images</a></li> <li><a href="/editing/keys">Keyboard Shortcuts</a></li> <li><a href="/editing/linking">Linking</a></li> <li><a href="/editing/math">Math Expressions</a></li> <li><a href="/editing/menu-paths">Menu Paths</a></li> <li><a href="/editing/navigation">Navigation</a></li> <li><a href="/editing/notices">Notices</a></li> <li><a href="/editing/people">People</a></li> <li><a href="/editing/pitfalls">Pitfalls</a></li> <li><a href="/editing/quizzes">Quizzes</a></li> <li><a href="/editing/statbox">Statbox</a></li> <li><a href="/editing/symbols">Symbols</a></li> <li><a href="/editing/tables">Tables</a></li> <li><a href="/editing/timelines">Timelines</a></li> <li><a href="/editing/tooltips">Tooltips</a></li> <li><a href="/editing/videos">Videos</a></li> <li><a href="/editing/whitespace">Whitespace</a></li> </ul></details></li>  </ul></details></li>  <li><details><summary><a href="/discuss">Discuss</a></summary><ul> <li><a href="/discuss/bugs">Reporting Issues</a></li> <li><a href="/discuss/mailing-lists">Mailing Lists</a></li> <li><a href="/discuss/chat">Chat</a></li> </ul></details></li>  <li><details><summary>Explore</summary><ul> <li><a href="/news">News</a></li> <li><details><summary><a href="/events">Events</a></summary><ul> <li><a href="/events/presentations">Presentations</a></li> <li><a href="/events/conferences">Conferences</a></li> <li><a href="/events/hackathons">Hackathons</a></li> <li><a href="/events">More...</a></li> </ul></details></li>  <li><details><summary><a href="/libs">Libraries</a></summary><ul> <li><a href="/libs/imagej-ops">ImageJ Ops</a></li> <li><a href="/libs/imagej-common">ImageJ Common</a></li> <li><a href="/libs/imagej-legacy">ImageJ Legacy</a></li> <li><a href="/libs/scijava">SciJava</a></li> <li><a href="/libs/scifio">SCIFIO</a></li> <li><details><summary><a href="/libs/imglib2">ImgLib2</a></summary><ul> <li><a href="/libs/imglib2/getting-started">Getting Started</a></li> <li><a href="/libs/imglib2/accessors">Accessors</a></li> <li><a href="/libs/imglib2/accessibles">Accessibles</a></li> <li><a href="/libs/imglib2/examples">Examples</a></li> <li><a href="/libs/imglib2/workshop-introductory">Introductory Workshop</a></li> <li><a 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> </ul> </div> </nav> <div id="dock-overlay-left" class="dock-overlay" data-dock-target="left-column"></div> <div id="dock-overlay-right" class="dock-overlay" data-dock-target="right-column"></div>  <div id="search-results"> <div id="search-hits"></div> <div id="pagination"></div> </div>   <script src="/assets/js/jquery.min.js"></script> <script src="/assets/js/jquery.scrolly.min.js"></script> <script src="/assets/js/browser.min.js"></script> <script src="/assets/js/breakpoints.min.js"></script> <script src="/assets/js/util.js"></script> <script src="/assets/js/jquery.toc.js"></script> <script src="/assets/js/lightbox.min.js"></script>   <script src="/assets/js/main.js"></script> <script src="/assets/js/dock.js"></script> <script src="/assets/js/code.js"></script>  <script src="https://cdn.jsdelivr.net/npm/anchor-js/anchor.min.js"></script> <script>anchors.add('#page h1, #page h2, #page h3, #page h4, #page h5, #page h6');</script>  <script src="https://cdn.jsdelivr.net/npm/citation-js@0.4.0-9"></script> <script src="/assets/js/cite.js"></script>  <script src="https://cdn.jsdelivr.net/npm/algoliasearch@4.13.0/dist/algoliasearch-lite.umd.js"></script> <script src="https://cdn.jsdelivr.net/npm/instantsearch.js@4.40.3/dist/instantsearch.production.min.js"></script> <script src="/assets/js/search.js"></script> <script src="/assets/js/search-tweaks.js"></script> </body> </html>

CINXE.COM

FIBSEM importer