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<!doctype html>
<html>
<head>
<meta charset="utf-8">
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<title>Image Analysis with Fiji by Jeremy Pike</title>
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<div class="wrapper">
<header>
<img src="https://rawgit.com/JeremyPike/image-analysis-with-fiji/master/COMPARE_logo.jpg" alt="COMPARE logo" style="width:275px">
<p></p>
<h1>Image Analysis with Fiji</h1>
<p>Introductory course for biologists</p>
<h2>Registration:</h2>
<p><b>Please register as a PPMS order to book a place:</b></p>
<p><a target="_blank" href="https://ppms.eu/bham/?COMPARE">25th April, In-person</a></p>
</header>
<section>
<h1>
<a id="author" class="anchor" href="#author" aria-hidden="true"><span class="octicon octicon-link"></span></a>Trainers</h1>
<p>Jeremy Pike, Image Analyst for <a target="_blank" href="http://www.birmingham-nottingham.ac.uk/compare/">COMPARE</a></p>
<p>Alessandro Di Maio, Microscopy lead for the <a target="_blank" href="https://www.birmingham.ac.uk/university/colleges/mds/facilities/technology-hub/microscopy-facility.aspx">Microscopy Facilities</a></p>
<h1>
<a id="summary" class="anchor" href="#summary" aria-hidden="true"><span class="octicon octicon-link"></span></a>Summary</h1>
<p><a target="_blank" href="http://imagej.net/ImageJ">Fiji/ImageJ</a> is a leading open-source image analysis application. This course will briefly cover introductory aspects of image processing and analysis theory, but will focus on practical sessions where participants will gain hands on experience.</p>
<h1>
<a id="audience" class="anchor" href="#audience" aria-hidden="true"><span class="octicon octicon-link"></span></a>Target Audience</h1>
<ul type="disk">
<li>The course is recommended for all researchers who use light microscopy.</li>
<li>This is an introductory course, designed for those with no, or limited experience, in bioimage analysis.</li>
<li>Graduate students, postdocs and staff members from the Universities of Birmingham and Nottingham, affiliated institutions and other external institutions or individuals.</li>
</ul>
<h1>
<a id="aims" class="anchor" href="#aims" aria-hidden="true"><span class="octicon octicon-link"></span></a>Aims and Objectives</h1>
<p>After this course participants should be able to:</p>
<ul type="disk">
<li>Perform basic image handling, manipulation and visualisation using Fiji. This will include working with multi-channel, z-stack and time-lapse data.</li>
<li>Understand and use meta-data, for example adding scale bars to images.</li>
<li>Load common microscopy formats using <a target="_blank" href="http://www.openmicroscopy.org/site/products/bio-formats">Bio-formats</a>.</li>
<li>Perform volume rendering using <a target="_blank" href="http://imagej.net/ClearVolume">ClearVolume</a>.</li>
<li>Use simple image analysis and processing techniques. To include automated thresholding, de-noising, spot detection and background subtraction.</li>
<li>Design and construct routine analysis workflows.</li>
<li>Perform batch processing using the ImageJ macro language (if time allows).</li>
<li>Find information online for further study. For example learning resources and forums.</li>
</ul>
<h1>
<a id="materials" class="anchor" href="#materials" aria-hidden="true"><span class="octicon octicon-link"></span></a>Course Materials</h1>
</h1>
<p>Note, this material was adapted from a course run at the Cancer Research UK Cambridge institute.</p>
<ul type="disk">
<li><a target="_blank" href="https://rawgit.com/JeremyPike/image-analysis-with-fiji/master/ImageAnalysisWithFijiSlides.pdf">Lecture Slides</a></li>
<li><a target="_blank" href="https://rawgit.com/JeremyPike/image-analysis-with-fiji/master/ImageAnalysisWithFijiExercises.pdf">Exercises</a></li>
<li><a target="_blank" href="https://bham-my.sharepoint.com/personal/j_a_pike_bham_ac_uk/_layouts/15/guestaccess.aspx?guestaccesstoken=dJ7L0ZJqs7OqlxW27xwX6v2%2b7K%2fslWSgjm0eOhKk2Nw%3d&docid=2_140449034cd2847739f2e25a309a9eae5&rev=1">Sample Data Zip file (~ 59Mb)</a></li>
<li><a target="_blank" href="https://rawgit.com/JeremyPike/image-analysis-with-fiji/master/macros/macroBatchProcessSolution.ijm">Batch processing macro</a></li>
<li><a target="_blank" href="https://rawgit.com/JeremyPike/image-analysis-with-fiji/master/macros/macroBatchProcessWithUI.ijm">Batch macro with user interface</a></li>
<li><a target="_blank" href="https://rawgit.com/JeremyPike/image-analysis-with-fiji/master/macros/macroZstackLabelSolution.ijm">Slice labelling macro</a></li>
</ul>
<h1>
<a id="software" class="anchor" href="#software" aria-hidden="true"><span class="octicon octicon-link"></span></a>Course Software</h1>
</h1>
<p>In this course participants will use Fiji and some of its plugins.</p>
<ul type="disk">
<li><a target="_blank" href="http://imagej.net/Fiji/Downloads">Fiji download</a></li>
<li><a target="_blank" href="http://imagej.net/ClearVolume">ClearVolume documentation</a></li>
<li><a target="_blank" href="http://bigwww.epfl.ch/algorithms/denoise/">PureDenoise documentation</a></li>
</ul>
</ul>
</section>
<footer>
<p>This project is maintained by <a href="https://github.com/JeremyPike">JeremyPike</a></p>
<p class="view"><a href="https://github.com/JeremyPike/image-analysis-with-fiji">View the Project on GitHub <small>JeremyPike/image-analysis-with-fiji</small></a></p>
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