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| 4 | +<!-- Generated by javadoc (21) on Sat Oct 03 04:14:11 UTC 2026 --> |
| 5 | +<title>All Packages (SNT 5.0.20 API)</title> |
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| 52 | +<div class="header"> |
| 53 | +<h1 title="All&nbsp;Packages" class="title">All Packages</h1> |
| 54 | +</div> |
| 55 | +<div class="caption"><span>Package Summary</span></div> |
| 56 | +<div class="summary-table two-column-summary"> |
| 57 | +<div class="table-header col-first">Package</div> |
| 58 | +<div class="table-header col-last">Description</div> |
| 59 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/package-summary.html">sc.fiji.snt</a></div> |
| 60 | +<div class="col-last even-row-color"> |
| 61 | +<div class="block">SNT core classes</div> |
| 62 | +</div> |
| 63 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/analysis/package-summary.html">sc.fiji.snt.analysis</a></div> |
| 64 | +<div class="col-last odd-row-color"> |
| 65 | +<div class="block">Analysis of <a href="sc/fiji/snt/Tree.html" title="class in sc.fiji.snt"><code>Tree</code></a>s.</div> |
| 66 | +</div> |
| 67 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/analysis/curation/package-summary.html">sc.fiji.snt.analysis.curation</a></div> |
| 68 | +<div class="col-last even-row-color"> |
| 69 | +<div class="block">Classes for curation of reconstructions, as implemented by the "Curation Assistant".</div> |
| 70 | +</div> |
| 71 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/analysis/detection/package-summary.html">sc.fiji.snt.analysis.detection</a></div> |
| 72 | +<div class="col-last odd-row-color"> |
| 73 | +<div class="block">Feature detectors for traced paths.</div> |
| 74 | +</div> |
| 75 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/analysis/graph/package-summary.html">sc.fiji.snt.analysis.graph</a></div> |
| 76 | +<div class="col-last even-row-color"> |
| 77 | +<div class="block">Classes for handling neuronal reconstructions as graphs</div> |
| 78 | +</div> |
| 79 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/analysis/growth/package-summary.html">sc.fiji.snt.analysis.growth</a></div> |
| 80 | +<div class="col-last odd-row-color"> |
| 81 | +<div class="block">Classes for growth analysis of neurites across time</div> |
| 82 | +</div> |
| 83 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/analysis/sholl/package-summary.html">sc.fiji.snt.analysis.sholl</a></div> |
| 84 | +<div class="col-last even-row-color"> |
| 85 | +<div class="block">Sholl analysis of Images, pre-sampled data and <a href="sc/fiji/snt/Tree.html" title="class in sc.fiji.snt"><code>Tree</code></a>s.</div> |
| 86 | +</div> |
| 87 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/analysis/sholl/gui/package-summary.html">sc.fiji.snt.analysis.sholl.gui</a></div> |
| 88 | +<div class="col-last odd-row-color"> |
| 89 | +<div class="block">GUI customizations (image overlays, plots, etc.) required for Sholl Analysis.</div> |
| 90 | +</div> |
| 91 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/analysis/sholl/math/package-summary.html">sc.fiji.snt.analysis.sholl.math</a></div> |
| 92 | +<div class="col-last even-row-color"> |
| 93 | +<div class="block">Statistical analysis of Sholl data</div> |
| 94 | +</div> |
| 95 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/analysis/sholl/parsers/package-summary.html">sc.fiji.snt.analysis.sholl.parsers</a></div> |
| 96 | +<div class="col-last odd-row-color"> |
| 97 | +<div class="block">Parsers to retrieve Sholl profiles from multiple sources (2D/3D images, |
| 98 | + reconstructions, and tables)</div> |
| 99 | +</div> |
| 100 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/annotation/package-summary.html">sc.fiji.snt.annotation</a></div> |
| 101 | +<div class="col-last even-row-color"> |
| 102 | +<div class="block">Classes handling neuropil annotations and atlases metadata.</div> |
| 103 | +</div> |
| 104 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/event/package-summary.html">sc.fiji.snt.event</a></div> |
| 105 | +<div class="col-last odd-row-color"> |
| 106 | +<div class="block">Utilities for TrakEM2 interaction</div> |
| 107 | +</div> |
| 108 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/filter/package-summary.html">sc.fiji.snt.filter</a></div> |
| 109 | +<div class="col-last even-row-color"> |
| 110 | +<div class="block">Filters for detection of tube-like structures</div> |
| 111 | +</div> |
| 112 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/gui/package-summary.html">sc.fiji.snt.gui</a></div> |
| 113 | +<div class="col-last odd-row-color"> |
| 114 | +<div class="block">Customizations and commands for SNT's GUI.</div> |
| 115 | +</div> |
| 116 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/gui/cmds/package-summary.html">sc.fiji.snt.gui.cmds</a></div> |
| 117 | +<div class="col-last even-row-color"> |
| 118 | +<div class="block">Scijava-based GUIs for SNT built-in commands.</div> |
| 119 | +</div> |
| 120 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/hyperpanes/package-summary.html">sc.fiji.snt.hyperpanes</a></div> |
| 121 | +<div class="col-last odd-row-color"> |
| 122 | +<div class="block">Classes implementing SNT's XY, ZY, and XZ canvases.</div> |
| 123 | +</div> |
| 124 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/io/package-summary.html">sc.fiji.snt.io</a></div> |
| 125 | +<div class="col-last even-row-color"> |
| 126 | +<div class="block">Classes for importing reconstructions into SNT.</div> |
| 127 | +</div> |
| 128 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/plugin/package-summary.html">sc.fiji.snt.plugin</a></div> |
| 129 | +<div class="col-last odd-row-color"> |
| 130 | +<div class="block">SNT add-ons as IJ2 commands</div> |
| 131 | +</div> |
| 132 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/plugin/ij1/package-summary.html">sc.fiji.snt.plugin.ij1</a></div> |
| 133 | +<div class="col-last even-row-color"> |
| 134 | +<div class="block">SNT add-ons as legacy ("IJ1") plugins.</div> |
| 135 | +</div> |
| 136 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/seed/package-summary.html">sc.fiji.snt.seed</a></div> |
| 137 | +<div class="col-last odd-row-color"> |
| 138 | +<div class="block">Classes for <a href="https://imagej.net/plugins/snt/seeds">Seed Tracing</a>.</div> |
| 139 | +</div> |
| 140 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/tracing/package-summary.html">sc.fiji.snt.tracing</a></div> |
| 141 | +<div class="col-last even-row-color"> |
| 142 | +<div class="block">Path-finding algorithms for interactive neuron tracing.</div> |
| 143 | +</div> |
| 144 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/tracing/artist/package-summary.html">sc.fiji.snt.tracing.artist</a></div> |
| 145 | +<div class="col-last odd-row-color"> |
| 146 | +<div class="block"><i>Artist</i> classes provide visual feedback for tracing algorithm execution.</div> |
| 147 | +</div> |
| 148 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/tracing/auto/package-summary.html">sc.fiji.snt.tracing.auto</a></div> |
| 149 | +<div class="col-last even-row-color"> |
| 150 | +<div class="block">Automatic neuron tracing algorithms that reconstruct complete neuronal |
| 151 | + morphologies from images without user interaction.</div> |
| 152 | +</div> |
| 153 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/tracing/auto/gwdt/package-summary.html">sc.fiji.snt.tracing.auto.gwdt</a></div> |
| 154 | +<div class="col-last odd-row-color"> |
| 155 | +<div class="block">Storage backends for the Gray-Weighted Distance Transform (GWDT) tracing |
| 156 | + algorithm.</div> |
| 157 | +</div> |
| 158 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/tracing/cost/package-summary.html">sc.fiji.snt.tracing.cost</a></div> |
| 159 | +<div class="col-last even-row-color"> |
| 160 | +<div class="block">Cost function implementations for classes implementing <a href="sc/fiji/snt/tracing/SearchInterface.html" title="interface in sc.fiji.snt.tracing"><code>SearchInterface</code></a></div> |
| 161 | +</div> |
| 162 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/tracing/heuristic/package-summary.html">sc.fiji.snt.tracing.heuristic</a></div> |
| 163 | +<div class="col-last odd-row-color"> |
| 164 | +<div class="block">Heuristic implementations for classes implementing <a href="sc/fiji/snt/tracing/SearchInterface.html" title="interface in sc.fiji.snt.tracing"><code>SearchInterface</code></a></div> |
| 165 | +</div> |
| 166 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/tracing/image/package-summary.html">sc.fiji.snt.tracing.image</a></div> |
| 167 | +<div class="col-last even-row-color"> |
| 168 | +<div class="block">Data structures used to keep track of encountered nodes during image-based searches for classes implementing |
| 169 | + <a href="sc/fiji/snt/tracing/SearchInterface.html" title="interface in sc.fiji.snt.tracing"><code>SearchInterface</code></a></div> |
| 170 | +</div> |
| 171 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/util/package-summary.html">sc.fiji.snt.util</a></div> |
| 172 | +<div class="col-last odd-row-color"> |
| 173 | +<div class="block">Miscellaneous SNT utilities, including classes defining reconstruction nodes.</div> |
| 174 | +</div> |
| 175 | +<div class="col-first even-row-color"><a href="sc/fiji/snt/viewer/package-summary.html">sc.fiji.snt.viewer</a></div> |
| 176 | +<div class="col-last even-row-color"> |
| 177 | +<div class="block">Visualization of reconstructions</div> |
| 178 | +</div> |
| 179 | +<div class="col-first odd-row-color"><a href="sc/fiji/snt/viewer/geditor/package-summary.html">sc.fiji.snt.viewer.geditor</a></div> |
| 180 | +<div class="col-last odd-row-color"> |
| 181 | +<div class="block">Classes implementing SNT's Graph Viewer</div> |
| 182 | +</div> |
| 183 | +</div> |
| 184 | +</main> |
| 185 | +<footer role="contentinfo"> |
| 186 | +<hr> |
| 187 | +<p class="legal-copy"><small>Copyright © 2010–2026 <a href="https://fiji.sc">Fiji</a>. All rights reserved.</small></p> |
| 188 | +</footer> |
| 189 | +</div> |
| 190 | +</div> |
| 191 | +</body> |
| 192 | +</html> |
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