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<title>flika: image processing for biologists — flika 0.2.25 documentation</title>
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<div class="section" id="flika-image-processing-for-biologists">
<h1>flika: image processing for biologists<a class="headerlink" href="#flika-image-processing-for-biologists" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
<p>flika makes it easy to write analyze images and movies of biological data. It is quick to
get started, and is easy to extend by installing a wide variety of plugins or writing your own.</p>
<img alt="_images/flika_screencapture.gif" src="_images/flika_screencapture.gif" />
<div class="section" id="install">
<h2>Install<a class="headerlink" href="#install" title="Permalink to this headline">¶</a></h2>
<p>Please see <a class="reference internal" href="getting-started.html#installation"><span class="std std-ref">Installation</span></a> for instructions. flika runs on Windows, OSX, and Linux.</p>
</div>
<div class="section" id="features">
<h2>Features<a class="headerlink" href="#features" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>Supports numerous types of image filetypes: .tif, .nd2, .stk, and more.</li>
<li>Record the steps of your analysis in a script to automate a series of flika commands.</li>
<li>Python 3</li>
<li>Rich plugin architecture, with many <a class="reference internal" href="plugins.html#extplugins"><span class="std std-ref">external plugins</span></a> and a growing community.</li>
<li>Open source under the <a class="reference internal" href="license.html#license"><span class="std std-ref">MIT license</span></a>.</li>
</ul>
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<div class="section" id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h2>
<p>Please see <a class="reference internal" href="contents.html#toc"><span class="std std-ref">Contents</span></a> for full documentation, including installation and tutorials.</p>
</div>
<div class="section" id="bugs-requests">
<h2>Bugs/Requests<a class="headerlink" href="#bugs-requests" title="Permalink to this headline">¶</a></h2>
<p>Please use the <a class="reference external" href="https://github.com/flika-org/flika/issues">GitHub issue tracker</a> to submit bugs or request features.</p>
</div>
<div class="section" id="changelog">
<h2>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h2>
<p>Consult the <a class="reference internal" href="changelog.html#changelog"><span class="std std-ref">Changelog</span></a> page for fixes and enhancements of each version.</p>
</div>
<div class="section" id="citations">
<h2>Citations<a class="headerlink" href="#citations" title="Permalink to this headline">¶</a></h2>
<p>flika was created to automatically identify and automate the analysis of local Ca <sup>2+</sup> signals but has grown into a general analysis tool for studying biological images. When using flika, please cite:</p>
<blockquote>
<div>Ellefsen, K., Settle, B., Parker, I. & Smith, I.
An algorithm for automated detection, localization
and measurement of local calcium signals from
camera-based imaging. Cell Calcium. 56:147-156, 2014</div></blockquote>
<p>Supported through National Institutes of Health grants GM 100201 to <a class="reference external" href="http://faculty.sites.uci.edu/ianfsmithlab/ismith/">Ian Smith</a>, and GM 048071 and 065830 to <a class="reference external" href="http://parkerlab.bio.uci.edu/members/ianparker.htm">Ian Parker</a>.</p>
</div>
<div class="section" id="authors">
<h2>Authors<a class="headerlink" href="#authors" title="Permalink to this headline">¶</a></h2>
<p>So far, code has been contributed by <a class="reference external" href="https://scitru.com/kyleellefsen">Kyle Ellefsen</a> , <a class="reference external" href="https://github.com/BrettJSettle">Brett Settle</a> and <a class="reference external" href="https://github.com/KevinTarhan">Kevin Tarhan</a>. If you would like to add your name to the list, see our guide for <a class="reference internal" href="contributing.html#contributing"><span class="std std-ref">contributing</span></a>.</p>
</div>
<div class="section" id="license">
<h2>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h2>
<p>Distributed under the terms of the <a class="reference internal" href="license.html#license"><span class="std std-ref">MIT license</span></a>, flika is free and open source software.</p>
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<img class="logo" src="_static/flika_logo.png" alt="Logo"/>
</a></p><h3>About flika</h3>
<p>
flika is an image processing program for biologists written in Python.
</p><h3><a href="#">Table Of Contents</a></h3>
<ul>
<li><a href="#">Home</a></li>
<li><a href="contents.html">Contents</a></li>
<li><a href="getting-started.html">Install</a></li>
<li><a href="example/index.html">Examples</a></li>
<li><a href="plugins.html">Plugins</a></li>
<li><a href="contributing.html">Contributing</a></li>
<li><a href="contact.html">Contact</a></li>
<li><a href="changelog.html">Changelog</a></li>
<li><a href="similar_projects.html">Similar Projects</a></li>
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<li><a href="api.html">API Reference</a></li>
</ul><h3>Useful Links</h3>
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<li><a href="https://github.com/flika-org/flika">GitHub</a></li>
<li><a href="https://pypi.python.org/pypi/flika">PyPI</a></li>
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