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<title>Welcome to Nornir’s documentation! — Nornir 1.3.1 documentation</title>
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<section id="welcome-to-nornir-s-documentation">
<h1>Welcome to Nornir’s documentation!<a class="headerlink" href="#welcome-to-nornir-s-documentation" title="Permalink to this headline">¶</a></h1>
<p>Nornir’s takes large sets of overlapping images in 2D and produces registered (a.k.a. aligned) 2D and 3D volumes of any size and scale.</p>
<p>The github repository for Nornir lives at <a class="reference external" href="http://github.com/nornir/">http://github.com/nornir/</a></p>
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<h2>Contents<a class="headerlink" href="#contents" title="Permalink to this headline">¶</a></h2>
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<h2>History<a class="headerlink" href="#history" title="Permalink to this headline">¶</a></h2>
<p>Nornir evolved from a collaboration between the <a class="reference external" href="http://prometheus.med.utah.edu/~marclab/marclab_09_science-papers.html/">Marc Lab</a> and the <a class="reference external" href="http://www.ucnia.org/">Scientific Computing Institute’s</a> Tasdizen and Whitaker groups at the University of Utah. The original tools, known as the <a class="reference external" href="http://www.ucnia.org/download/ncrtoolset/">NCR Toolset</a> were used to construct <a class="reference external" href="http://www.ncbi.nlm.nih.gov/pubmed/21311605/">RC1</a>, a 250um diameter, 33um tall cylinder of rabbit retina at a resoultion of 2.18 nm/pixel.</p>
<p>Nornir is a work in progress. It currently supports importing images from transmission electron microscopes running SerialEM (.idoc files), light microscopes running Surveyor (.pmg files), and other volumes represented with a single image per section (.png files).</p>
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<h2>System requirements<a class="headerlink" href="#system-requirements" title="Permalink to this headline">¶</a></h2>
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<h2>Related Tools<a class="headerlink" href="#related-tools" title="Permalink to this headline">¶</a></h2>
<p>Volume images frequently exceed the reasonable sizes for single images. <a class="reference external" href="http://connectomes.utah.edu/">Viking</a> is another Marc lab tool for viewing and annotating huge datasets. Nornir produces volumes that can be viewed using Viking if placed on a web server.</p>
<p>Analysis of the annotations created by Viking for our existing rabbit connectome and future connectomes is performed by the <a class="reference external" href="https://github.com/jamesra/py-connectome-analysis/wiki">py-connectome-analysis</a> package</p>
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