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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<title>Installation — ClearMap 0.9.2 documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="introduction.html">Overview of ClearMap</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="">Installation</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#requirements">Requirements</a></li>
<li class="toctree-l2"><a class="reference internal" href="#id1">Installation</a></li>
<li class="toctree-l2"><a class="reference internal" href="#configuration">Configuration</a></li>
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<div class="section" id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
<div class="section" id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this headline">¶</a></h2>
<p>ClearMap is written in Python 2.7. It should run on any Python environment, but it also relies on external softwares such as <a class="reference external" href="http://elastix.isi.uu.nl">Elastix</a> which may not run optimally on Windows or Apple systems.
For typical use, we recommend a workstation running Ubuntu 14 or later with at least 4 CPU cores, 64Gb of RAM and SSD disks. 128Gb of RAM and 6 cores or above will have much increased performances. The processing time however will depend greatly on the parameters set, so your experience may be different. Also, large hard drives may be needed to host the raw data, although 1 to 4Tb of storage space should be enough for most users.</p>
</div>
<div class="section" id="id1">
<h2>Installation<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
<p>To install ClearMap, first create a folder to contain all the files for the program. Download the scripts from the latest version of ClearMap from <a class="reference external" href="https://www.idisco.info">The iDISCO website</a> and extract them in the ClearMap folder. You also need to download individually the following softwares:</p>
<blockquote>
<div><ul class="simple">
<li>To do the alignement, you should download <a class="reference external" href="http://elastix.isi.uu.nl">Elastix</a> (<a class="reference external" href="http://elastix.isi.uu.nl">http://elastix.isi.uu.nl</a>)</li>
<li>If you wish to use the machine learning filters, download <a class="reference external" href="http://ilastik.org">Ilastik</a> (<a class="reference external" href="http://ilastik.org">http://ilastik.org</a>). This is an optional download, only if you wish to use this more complete object detection framework for complex objects.</li>
</ul>
</div></blockquote>
<p>If you’re starting from a fresh Ubuntu 16.04LTS install, for instance, here are the steps to complete the installation. Open a terminal window and type the following instructions:</p>
<ul class="simple">
<li>Installation tools:</li>
</ul>
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>sudo apt-get update
<span class="nv">$ </span>sudo apt-get install git
<span class="nv">$ </span>sudo apt-get install python-pip
<span class="nv">$ </span>sudo -H pip install --upgrade pip
</pre></div>
</div>
<ul class="simple">
<li>Download ClearMap:</li>
</ul>
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>git clone https://github.com/ChristophKirst/ClearMap.git
</pre></div>
</div>
<ul class="simple">
<li>Install Spyder:</li>
</ul>
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>sudo apt-get install spyder
</pre></div>
</div>
<ul class="simple">
<li>Install the necessary libraries:</li>
</ul>
<div class="highlight-bash"><div class="highlight"><pre><span class="nv">$ </span>sudo apt-get install python-opencv
<span class="nv">$ </span>sudo apt-get install cython
<span class="nv">$ </span>sudo apt-get install python-tifffile
<span class="nv">$ </span>sudo apt-get install python-h5py
<span class="nv">$ </span>sudo apt-get install python-natsort
<span class="nv">$ </span>sudo -H pip install scikit-image
</pre></div>
</div>
<p>We use <a class="reference external" href="https://pythonhosted.org/spyder/">Spyder</a> to run the code. Set the project explorer and working environment in the ClearMap folder.</p>
</div>
<div class="section" id="configuration">
<h2>Configuration<a class="headerlink" href="#configuration" title="Permalink to this headline">¶</a></h2>
<p>Open the file <code class="docutils literal"><span class="pre">ClearMap/Settings.py</span></code> to set the paths of installations for Ilastik and Elastix:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">IlastikPath</span> <span class="o">=</span> <span class="s">'/yourpath/ilastik'</span><span class="p">;</span>
<span class="gp">>>> </span><span class="n">ElastixPath</span> <span class="o">=</span> <span class="s">'/yourpath/elastix'</span><span class="p">;</span>
</pre></div>
</div>
<p>Note that Ilastik is optional. If you haven’t installed it, you can set the path to <code class="docutils literal"><span class="pre">None</span></code>. You can also set the installation to run on multiple machines by setting a host specific path:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="k">if</span> <span class="n">hostname</span> <span class="o">==</span> <span class="s">'kagalaska.nld'</span><span class="p">:</span> <span class="c">#Christoph’s Laptop</span>
<span class="gp">>>> </span> <span class="n">IlastikPath</span> <span class="o">=</span> <span class="s">'/home/ckirst/programs/ilastik/'</span><span class="p">;</span>
<span class="gp">>>> </span> <span class="n">ElastixPath</span> <span class="o">=</span> <span class="s">'/home/ckirst/programs/elastix/'</span><span class="p">;</span>
<span class="gp">>>> </span><span class="k">elif</span> <span class="n">hostname</span> <span class="o">==</span> <span class="s">'mtllab-Ubuntu'</span><span class="p">:</span> <span class="c">#Nico’s Workstation</span>
<span class="gp">>>> </span> <span class="n">IlastikPath</span> <span class="o">=</span> <span class="s">'/usr/local/ilastik'</span><span class="p">;</span>
<span class="gp">>>> </span> <span class="n">ElastixPath</span> <span class="o">=</span> <span class="s">'/usr/local/elastix'</span><span class="p">;</span>
</pre></div>
</div>
</div>
<div class="section" id="additionnal-informations">
<h2>Additionnal Informations:<a class="headerlink" href="#additionnal-informations" title="Permalink to this headline">¶</a></h2>
<p>We run ClearMap on Ubuntu 16.04LTS using the following libraries:</p>
<ul class="simple">
<li>Matplotlib 1.5.1</li>
<li>Numpy 1.11.0</li>
<li>Scipy 0.16.0</li>
<li>Skimage 0.12.3</li>
<li>Mahotas 1.3.0 (<a class="reference external" href="http://luispedro.org/software/mahotas/">website</a>)</li>
<li>h5py 2.6.0 (for Imaris files input/output only)</li>
<li>openCV 2.4.9.1</li>
<li>PyQt4</li>
<li>tifffile 0.6.2</li>
<li>Cython 0.23.1</li>
</ul>
</div>
</div>
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