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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<html xmlns="http://www.w3.org/1999/xhtml">
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>ClearMap — ClearMap 0.9.2 documentation</title>
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<p style="font-size: 30px; color: color: #11557C"> <a href="#" style="color: #11557C; font-weight: bold">ClearMap iDISCO+ Toolbox Documentation</a></p>
<a href="#"><img src="_static/brain_bw_small.jpg" height=50px width=150% border="0" alt="ClearMap"/></a>
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<div class="related" role="navigation" aria-label="related navigation">
<h3>Navigation</h3>
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<li class="right" style="margin-right: 10px">
<a href="genindex.html" title="General Index"
accesskey="I">index</a></li>
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<h3><a href="#">Table Of Contents</a></h3>
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<li class="toctree-l1"><a class="reference internal" href="introduction.html">Overview of ClearMap</a></li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="imageanalysis.html">ClearMap Image Analysis Tools</a></li>
<li class="toctree-l1"><a class="reference internal" href="roadmap.html">Roadmap</a></li>
<li class="toctree-l1"><a class="reference internal" href="issues.html">Issues</a></li>
</ul>
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<p class="topless"><a href="introduction.html"
title="next chapter">Overview of ClearMap</a></p>
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<div class="section" id="clearmap">
<h1>ClearMap<a class="headerlink" href="#clearmap" title="Permalink to this headline">¶</a></h1>
<p><em>ClearMap</em> is a toolbox for the analysis and registration of volumetric data
from cleared tissues.</p>
<p><em>ClearMap</em> has been designed to analyze large 3D image stack datasets obtained with Light Sheet Microscopy
of iDISCO+ cleared mouse brains samples immunolabeled for nuclear proteins. ClearMap can perform image registration to a 3D annotated reference (such as the Allen Institute Brain Atlases), volumetric image processing, object detection and statistical analysis. The tools in <em>ClearMap</em> have been written with the mapping of Immediate Early Genes in the brain as the primary application.</p>
<p>However, these tools should also be more broadly useful for data obtained with other types of microscopes, other types of markers, and other clearing techniques. Moreover, the registration and region segmentation capabilities of ClearMap are not depending on the Atlases and annotations we used in our study. Users are free to import their own reference files and annotation files, so the use of <em>ClearMap</em> can be expanded to other species, and other organs or samples.</p>
<p><em>ClearMap</em> is written in Python 2.7, and is designed to take advantage of parallel processing capabilities of modern workstations. We hope the open structure of the code will enable in the future many new modules to be added to ClearMap to broaden the range of applications to different types of biological objects or structures.</p>
<div class="section" id="author-and-license">
<h2>Author and License<a class="headerlink" href="#author-and-license" title="Permalink to this headline">¶</a></h2>
<div class="section" id="authors">
<h3>Authors:<a class="headerlink" href="#authors" title="Permalink to this headline">¶</a></h3>
<div class="section" id="clearmap-lead-programming-and-design">
<h4>ClearMap lead programming and design:<a class="headerlink" href="#clearmap-lead-programming-and-design" title="Permalink to this headline">¶</a></h4>
<p>Christoph Kirst,
<em>The Rockefeller University</em></p>
</div>
<div class="section" id="scripts-and-specific-applications">
<h4>Scripts and specific applications:<a class="headerlink" href="#scripts-and-specific-applications" title="Permalink to this headline">¶</a></h4>
<p>Nicolas Renier and Christoph Kirst
<em>The Rockefeller University</em></p>
</div>
<div class="section" id="documentation">
<h4>Documentation:<a class="headerlink" href="#documentation" title="Permalink to this headline">¶</a></h4>
<p>Christoph Kirst and Nicolas Renier
<em>The Rockefeller University</em></p>
</div>
<div class="section" id="additional-programming-and-consulting">
<h4>Additional programming and consulting:<a class="headerlink" href="#additional-programming-and-consulting" title="Permalink to this headline">¶</a></h4>
<p>Kannan Umadevi Venkataraju
<em>Cold Spring Harbor Laboratories</em></p>
</div>
</div>
<div class="section" id="license">
<h3>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h3>
<p>GNU GENERAL PUBLIC LICENSE Version 3</p>
<p>See <a class="reference download internal" href="_downloads/LICENSE.txt"><code class="xref download docutils literal"><span class="pre">LICENSE</span></code></a> or <a class="reference external" href="http://www.gnu.org/licenses/gpl-3.0.en.html">gnu.org</a> for details.</p>
</div>
</div>
<div class="section" id="using-clearmap">
<h2>Using ClearMap<a class="headerlink" href="#using-clearmap" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="introduction.html">Overview of ClearMap</a><ul>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#io">IO</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#alignment">Alignment</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#image-processing">Image Processing</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#analysis">Analysis</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#idisco-clearing-method">iDISCO+ Clearing Method</a></li>
<li class="toctree-l2"><a class="reference internal" href="introduction.html#references">References</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="installation.html#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#id1">Installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#configuration">Configuration</a></li>
<li class="toctree-l2"><a class="reference internal" href="installation.html#additionnal-informations">Additionnal Informations:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a><ul>
<li class="toctree-l2"><a class="reference internal" href="tutorial.html#the-parameter-file">The Parameter File</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial.html#the-run-file">The Run File</a></li>
<li class="toctree-l2"><a class="reference internal" href="tutorial.html#analysis-tools">Analysis Tools</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="imageanalysis.html">ClearMap Image Analysis Tools</a><ul>
<li class="toctree-l2"><a class="reference internal" href="imageanalysis.html#visualizing-3d-images">Visualizing 3D Images</a></li>
<li class="toctree-l2"><a class="reference internal" href="imageanalysis.html#image-statistics">Image Statistics</a></li>
<li class="toctree-l2"><a class="reference internal" href="imageanalysis.html#background-removal">Background Removal</a></li>
<li class="toctree-l2"><a class="reference internal" href="imageanalysis.html#image-filter">Image Filter</a></li>
<li class="toctree-l2"><a class="reference internal" href="imageanalysis.html#maxima-detection">Maxima Detection</a></li>
<li class="toctree-l2"><a class="reference internal" href="imageanalysis.html#cell-shape-detection">Cell Shape Detection</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="roadmap.html">Roadmap</a><ul>
<li class="toctree-l2"><a class="reference internal" href="roadmap.html#plans-for-future-developoment">Plans for future developoment:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="issues.html">Issues</a></li>
</ul>
</div>
</div>
<div class="section" id="clearmap-functions">
<h2>ClearMap functions<a class="headerlink" href="#clearmap-functions" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="api/ClearMap.html">ClearMap package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="api/ClearMap.html#subpackages">Subpackages</a></li>
</ul>
</li>
</ul>
</div>
</div>
</div>
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<h3>Navigation</h3>
<ul>
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<a href="genindex.html" title="General Index"
>index</a></li>
<li class="right" >
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>modules</a> |</li>
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© Copyright 2016 Christoph Kirst.
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