-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathoverview.html
More file actions
172 lines (151 loc) · 10.4 KB
/
Copy pathoverview.html
File metadata and controls
172 lines (151 loc) · 10.4 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
<!DOCTYPE html>
<html class="writer-html5" lang="en" data-content_root="./">
<head>
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview — Nornir 1.7.6 documentation</title>
<link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
<link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=9edc463e" />
<script src="_static/jquery.js?v=5d32c60e"></script>
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
<script src="_static/documentation_options.js?v=6cfcd222"></script>
<script src="_static/doctools.js?v=9bcbadda"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="_static/js/theme.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Concepts" href="concepts.html" />
<link rel="prev" title="Host requirements" href="host_requirements.html" />
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search" >
<a href="index.html" class="icon icon-home">
Nornir
</a>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
<p class="caption" role="heading"><span class="caption-text">Start</span></p>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="start.html">Start here</a></li>
<li class="toctree-l1"><a class="reference internal" href="host_requirements.html">Host requirements</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Overview</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#mission">Mission</a></li>
<li class="toctree-l2"><a class="reference internal" href="#history">History</a></li>
<li class="toctree-l2"><a class="reference internal" href="#related-tools">Related tools</a></li>
<li class="toctree-l2"><a class="reference internal" href="#system-notes">System notes</a></li>
<li class="toctree-l2"><a class="reference internal" href="#terminology">Terminology</a></li>
</ul>
</li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Concepts</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="concepts.html">Concepts</a></li>
<li class="toctree-l1"><a class="reference internal" href="overview_alignment_theory.html">Overview of volume building</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Guides</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="guides/index.html">Guides</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Agents and contributors</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="agents.html">Agents and contributors</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Performance</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="performance/index.html">Performance</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Reference</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="packages/index.html">Packages</a></li>
<li class="toctree-l1"><a class="reference internal" href="pipelines.html">Pipeline catalogue</a></li>
<li class="toctree-l1"><a class="reference internal" href="api/index.html">API reference</a></li>
<li class="toctree-l1"><a class="reference internal" href="docker/index.html">Docker images</a></li>
<li class="toctree-l1"><a class="reference internal" href="development/index.html">Development</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">Nornir</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="Page navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
<li class="breadcrumb-item active">Overview</li>
<li class="wy-breadcrumbs-aside">
<a href="_sources/overview.rst.txt" rel="nofollow"> View page source</a>
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<section id="overview">
<h1>Overview<a class="headerlink" href="#overview" title="Link to this heading"></a></h1>
<p>Nornir is a collection of Python packages for building image mosaics and 3D volumes from serial-section imaging data. Components cover thread/process pools, shared utilities, image registration, and volume construction.</p>
<section id="mission">
<h2>Mission<a class="headerlink" href="#mission" title="Link to this heading"></a></h2>
<p>Nornir’s goal is to take large sets of overlapping images in 2D and 3D and produce <strong>registered</strong> (aligned) 2D and 3D volumes at any practical size and scale.</p>
<p><strong>Theory and figures:</strong> for a guided walkthrough of mosaic capture, tile alignment, slice-to-slice registration, and volume mapping—with the original figures from the public manual—see <a class="reference internal" href="overview_alignment_theory.html"><span class="doc">Overview of volume building</span></a>.</p>
<p><strong>Documentation convention:</strong> narrative and API reference for the umbrella project live in this monodoc. Each <code class="docutils literal notranslate"><span class="pre">nornir-*</span></code> package also has a short <code class="docutils literal notranslate"><span class="pre">README.md</span></code> at its repository root with an introduction and links back here.</p>
</section>
<section id="history">
<h2>History<a class="headerlink" href="#history" title="Link to this heading"></a></h2>
<p>Nornir evolved from a collaboration between the <a class="reference external" href="https://prometheus.med.utah.edu/~marclab/marclab_09_science-papers.html">Marc Lab</a> and the <a class="reference external" href="https://www.ucnia.org/">Scientific Computing Institute</a> (Tasdizen and Whitaker groups) at the University of Utah. The original tools, known as the <a class="reference external" href="https://www.ucnia.org/download/ncrtoolset/">NCR Toolset</a>, were used to construct <a class="reference external" href="https://pubmed.ncbi.nlm.nih.gov/21311605/">RC1</a>, a 250 µm diameter, 33 µm tall cylinder of rabbit retina at a resolution of 2.18 nm/pixel.</p>
<p>Nornir is a work in progress. It supports importing images from transmission electron microscopes running SerialEM (<code class="docutils literal notranslate"><span class="pre">.idoc</span></code> files), light microscopes running Surveyor (<code class="docutils literal notranslate"><span class="pre">.pmg</span></code> files), and other volumes represented with a single image per section (<code class="docutils literal notranslate"><span class="pre">.png</span></code> files).</p>
</section>
<section id="related-tools">
<h2>Related tools<a class="headerlink" href="#related-tools" title="Link to this heading"></a></h2>
<p>Volume images frequently exceed a reasonable size for a single file. Nornir builds the aligned volume and a VikingXML manifest. <strong>Viking</strong> views and annotates that volume when the output is placed on a web server. <strong>SBFSEM-tools</strong> analyzes Viking annotations in MATLAB. Build in Nornir, view and annotate in Viking, analyze in SBFSEM-tools.</p>
<ul class="simple">
<li><p><a class="reference external" href="https://github.com/connectomes/Viking">Viking</a></p></li>
<li><p><a class="reference external" href="https://github.com/neitzlab/SBFSEM-tools">SBFSEM-tools</a></p></li>
</ul>
<p>See <a class="reference internal" href="guides/build_volume.html"><span class="doc">Build a volume</span></a>.</p>
</section>
<section id="system-notes">
<h2>System notes<a class="headerlink" href="#system-notes" title="Link to this heading"></a></h2>
<p>What a machine needs to run Pyre, a workstation pipeline, or Docker is in <a class="reference internal" href="host_requirements.html"><span class="doc">Host requirements</span></a>. Production volumes (NAS, scratch disk, GPU class) are in <a class="reference internal" href="performance/envelope.html"><span class="doc">Production envelope</span></a>.</p>
</section>
<section id="terminology">
<h2>Terminology<a class="headerlink" href="#terminology" title="Link to this heading"></a></h2>
<p>Terms used across the manual (block, section, mosaic, tile, channel, filter, prune, blob, STOS, grid, slice-to-volume) are defined in <a class="reference internal" href="concepts.html"><span class="doc">Concepts</span></a>.</p>
</section>
</section>
</div>
</div>
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
<a href="host_requirements.html" class="btn btn-neutral float-left" title="Host requirements" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
<a href="concepts.html" class="btn btn-neutral float-right" title="Concepts" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
</div>
<hr/>
<div role="contentinfo">
<p>© Copyright Nornir contributors.</p>
</div>
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
provided by <a href="https://readthedocs.org">Read the Docs</a>.
</footer>
</div>
</div>
</section>
</div>
<script>
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>