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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8"/>
<title></title>
<meta name="generator" content="LibreOffice 4.3.3.2 (Linux)"/>
<meta name="created" content="2017-03-01T12:36:55.590730789"/>
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<h2 class="western"><a name="Designdocument:morphologycomponentofSDK-FeaturedefinitionsandassociatedAPIcalls"></a>
<strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="4" style="font-size: 15pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">Feature
definitions and associated API calls</span></span></span></font></font></font></span></strong></h2>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Features
are based on rotated but unscaled morphologies. Except as otherwise
noted, there is an implicit "_x", "_y" and "_z"
on feature names for spatial features calculated along each axis.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">A
compartment is defined as the conical section between two SWC nodes.
A compartment's type is the type of its non-root node (ie, the node
furthest from the root).</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Trifurcations
are treated as adjacent bifurcations.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Features
are calculated separately for apical dendrite, basal dendrite, all
dendrites, axon, and all neurites. This generates 5 sets of features
per morphology.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">MorphologyFeatures::calculate()
– Calculates features only on the neurite branches that can be
traced back to the soma (i.e., that have the soma as their root)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">MorphologyFeatures::calculate_cloud()
– Calculates a subset of features that are relevant to analyzing a
disconnected tree (e.g., an axon missing many segments)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-first_compartment_moment"></a>
<strong><em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>first_compartment_moment</b></span></span></font></font></font></span></em></strong></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
centroid of all compartments along each axis:</font></font></font></p>
<p align="left" style="margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; line-height: 0.21in; orphans: 1; text-decoration: none"><a name="MathJax-Element-2-Frame"></a><a name="MathJax-Span-3"></a><a name="MathJax-Span-4"></a><a name="MathJax-Span-5"></a><a name="MathJax-Span-6"></a><a name="MathJax-Span-7"></a><a name="MathJax-Span-8"></a><a name="MathJax-Span-9"></a><a name="MathJax-Span-10"></a><a name="MathJax-Span-11"></a><a name="MathJax-Span-12"></a><a name="MathJax-Span-13"></a><a name="MathJax-Span-14"></a><a name="MathJax-Span-15"></a><a name="MathJax-Span-16"></a><a name="MathJax-Span-17"></a><a name="MathJax-Span-18"></a><a name="MathJax-Span-19"></a><a name="MathJax-Span-20"></a><a name="MathJax-Span-21"></a><a name="MathJax-Span-22"></a><a name="MathJax-Span-23"></a><a name="MathJax-Span-24"></a><a name="MathJax-Span-25"></a><a name="MathJax-Span-26"></a><a name="MathJax-Span-27"></a><a name="MathJax-Span-28"></a><a name="MathJax-Span-29"></a><a name="MathJax-Span-30"></a><a name="MathJax-Span-31"></a><a name="MathJax-Span-32"></a><a name="MathJax-Span-33"></a><a name="MathJax-Span-34"></a><a name="MathJax-Span-35"></a><a name="MathJax-Span-36"></a><a name="MathJax-Span-37"></a><a name="MathJax-Span-38"></a><a name="MathJax-Span-39"></a>
<span style="display: inline-block; border: none; padding: 0in"><font color="#333333">∑<font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">=1</span></span></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">n</span></i></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">P</span></i></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="Arial, sans-serif"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">∗</span></span></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">L</span></i></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="Arial, sans-serif"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">∑</span></span></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">=1</span></span></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">n</span></i></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">L</span></i></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font></span></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">for
n compartments, where Pi is the spatial position of compartment i's
center along the measured axis, and Li is the length of compartment
i.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">NOTE:
The radius of each compartment is not used for this calculation. All
compartments are treated as having unit radius, allowing only
compartment length to be in the moment equation.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">API
function: </span></span></span></font></font></font></span><strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">calculate_compartment_moments</span></span></span></font></font></font></span></strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">(morph)</span></span></span></font></font></font></span></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-second_compartment_moment"></a>
<strong><em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>second_compartment_moment</b></span></span></font></font></font></span></em></strong></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
second moment (variance) of all compartments along each axis:</font></font></font></p>
<p align="left" style="margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; line-height: 0.21in; orphans: 1; text-decoration: none"><a name="MathJax-Element-3-Frame"></a><a name="MathJax-Span-40"></a><a name="MathJax-Span-41"></a><a name="MathJax-Span-42"></a><a name="MathJax-Span-43"></a><a name="MathJax-Span-44"></a><a name="MathJax-Span-45"></a><a name="MathJax-Span-46"></a><a name="MathJax-Span-47"></a><a name="MathJax-Span-48"></a><a name="MathJax-Span-49"></a><a name="MathJax-Span-50"></a><a name="MathJax-Span-51"></a><a name="MathJax-Span-52"></a><a name="MathJax-Span-53"></a><a name="MathJax-Span-54"></a><a name="MathJax-Span-55"></a><a name="MathJax-Span-56"></a><a name="MathJax-Span-57"></a><a name="MathJax-Span-58"></a><a name="MathJax-Span-59"></a><a name="MathJax-Span-60"></a><a name="MathJax-Span-61"></a><a name="MathJax-Span-62"></a><a name="MathJax-Span-63"></a><a name="MathJax-Span-64"></a><a name="MathJax-Span-65"></a><a name="MathJax-Span-66"></a><a name="MathJax-Span-67"></a><a name="MathJax-Span-68"></a><a name="MathJax-Span-69"></a><a name="MathJax-Span-70"></a><a name="MathJax-Span-71"></a><a name="MathJax-Span-72"></a><a name="MathJax-Span-73"></a><a name="MathJax-Span-74"></a><a name="MathJax-Span-75"></a><a name="MathJax-Span-76"></a><a name="MathJax-Span-77"></a><a name="MathJax-Span-78"></a><a name="MathJax-Span-79"></a><a name="MathJax-Span-80"></a><a name="MathJax-Span-81"></a><a name="MathJax-Span-82"></a><a name="MathJax-Span-83"></a><a name="MathJax-Span-84"></a>
<span style="display: inline-block; border: none; padding: 0in"><font color="#333333">∑<font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">=1</span></span></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">n</span></i></font></font><font face="MathJax Main"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">(</span></span></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">P</span></i></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">0</span></span></font></font><font face="Arial, sans-serif"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">−</span></span></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">P</span></i></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="MathJax Main"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">)</span></span></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">2</span></span></font></font><font face="Arial, sans-serif"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">∗</span></span></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">L</span></i></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="Arial, sans-serif"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">∑</span></span></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">=1</span></span></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">n</span></i></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">L</span></i></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font></span></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">for
n compartments, where Pi is the spatial position of compartment i's
center along the measured axis, P0 is the centroid of the dendrite
along this axis (</span></span></span></font></font></font></span><em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_component_moment</span></span></span></font></font></font></span></em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">),
and Li is the length of compartment i.</span></span></span></font></font></font></span></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">NOTE:
The radius of each compartment is not used for this calculation. All
compartments are treated as having unit radius, allowing only
compartment length to be in the moment equation.</span></span></span></font></font></font></span></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">API
function: </span></span></span></font></font></font></span><strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">calculate_compartment_moments</span></span></span></font></font></font></span></strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">(morph)</span></span></span></font></font></font></span></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-first_bifurcation_moment"></a>
<strong><em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>first_bifurcation_moment</b></span></span></font></font></font></span></em></strong></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
centroid position of all bifurcation along each axis:</font></font></font></p>
<p align="left" style="margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; line-height: 0.21in; orphans: 1; text-decoration: none"><a name="MathJax-Element-4-Frame"></a><a name="MathJax-Span-85"></a><a name="MathJax-Span-86"></a><a name="MathJax-Span-87"></a><a name="MathJax-Span-88"></a><a name="MathJax-Span-89"></a><a name="MathJax-Span-90"></a><a name="MathJax-Span-91"></a><a name="MathJax-Span-92"></a><a name="MathJax-Span-93"></a><a name="MathJax-Span-94"></a><a name="MathJax-Span-95"></a><a name="MathJax-Span-96"></a><a name="MathJax-Span-97"></a><a name="MathJax-Span-98"></a><a name="MathJax-Span-99"></a><a name="MathJax-Span-100"></a><a name="MathJax-Span-101"></a><a name="MathJax-Span-102"></a><a name="MathJax-Span-103"></a>
<span style="display: inline-block; border: none; padding: 0in"><font color="#333333">∑<font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">=1</span></span></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">n</span></i></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">P</span></i></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">in</span></i></font></font></span></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">for
n bifurcating nodes (ie, nodes with two or more children), where Pi
is the spatial position of node i along the measured axis.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">API
function: </span></span></span></font></font></font></span><strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">calculate_bifurcation_moments</span></span></span></font></font></font></span></strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">(morph)</span></span></span></font></font></font></span></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-second_bifurcation_moment"></a>
<strong><em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>second_bifurcation_moment</b></span></span></font></font></font></span></em></strong></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
second moment (variance) of bifurcation locations along each axis:</font></font></font></p>
<p align="left" style="margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; line-height: 0.21in; orphans: 1; text-decoration: none"><a name="MathJax-Element-5-Frame"></a><a name="MathJax-Span-104"></a><a name="MathJax-Span-105"></a><a name="MathJax-Span-106"></a><a name="MathJax-Span-107"></a><a name="MathJax-Span-108"></a><a name="MathJax-Span-109"></a><a name="MathJax-Span-110"></a><a name="MathJax-Span-111"></a><a name="MathJax-Span-112"></a><a name="MathJax-Span-113"></a><a name="MathJax-Span-114"></a><a name="MathJax-Span-115"></a><a name="MathJax-Span-116"></a><a name="MathJax-Span-117"></a><a name="MathJax-Span-118"></a><a name="MathJax-Span-119"></a><a name="MathJax-Span-120"></a><a name="MathJax-Span-121"></a><a name="MathJax-Span-122"></a><a name="MathJax-Span-123"></a><a name="MathJax-Span-124"></a><a name="MathJax-Span-125"></a><a name="MathJax-Span-126"></a><a name="MathJax-Span-127"></a><a name="MathJax-Span-128"></a><a name="MathJax-Span-129"></a><a name="MathJax-Span-130"></a>
<span style="display: inline-block; border: none; padding: 0in"><font color="#333333">∑<font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">=1</span></span></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">n</span></i></font></font><font face="MathJax Main"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">(</span></span></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">P</span></i></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">0</span></span></font></font><font face="Arial, sans-serif"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">−</span></span></font></font><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i><span style="font-weight: normal">P</span></i></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">i</span></i></font></font><font face="MathJax Main"><font size="3" style="font-size: 12pt"><span style="font-style: normal"><span style="font-weight: normal">)</span></span></font></font><font face="MathJax Main"><font size="2" style="font-size: 9pt"><span style="font-style: normal"><span style="font-weight: normal">2</span></span></font></font><font face="MathJax Math"><font size="2" style="font-size: 9pt"><i><span style="font-weight: normal">n</span></i></font></font></span></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">for
n bifurcating nodes (ie, nodes with two or more children), where P0
is the bifurcation centroid along the axis (</span></span></span></font></font></font></span><em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_bifurcation_moment</span></span></span></font></font></font></span></em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">)
and Pi is the spatial position of node i along the measured axis.</span></span></span></font></font></font></span></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">API
function: </span></span></span></font></font></font></span><strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">calculate_bifurcation_moments</span></span></span></font></font></font></span></strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">(morph)</span></span></span></font></font></font></span></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-max_euclidean_distance"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>max_euclidean_distance</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
spatial distance from the soma to the most distal node.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_max_euclidean_distance(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-max_path_distance"></a>
<em><strong><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>max_path_distance</b></span></span></font></font></font></span></strong></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
path distance from the soma to the furthest neurite tip. This is the
longest path between soma and tip. It is NOT the path distance to the
neurite having the maximal euclidean distance.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_max_path_distance(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Differs
from V3D. Manually examined SWC. V3D number includes diameter of soma
(ie, distance from soma center to axon/dendrite root).</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-num_stems"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>num_stems</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
number of stems sprouting from the soma.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
functions: calculate_num_stems(morph);
calculate_num_stems_by_type(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Matches
V3D</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-num_bifurcations"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>num_bifurcations</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
number of bifurcations (i.e., nodes with two children) that exist in
the morphology. A trifurcation is treated as two neighboring
bifurcations, to avoid artifacts arising from segmenting and segment
sizes. Stems from the soma are not included in this calculation.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_num_bifurcations(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Discrepancy
w/ V3D. Manually examined
/projects/mousecelltypes/vol1/prod250/specimen_341442651/Pvalb-IRES-Cre_Ai14-178310.02.01.01_491119993_m.swc.
Number of bifurcations are as reported by new algorithm (ie, V3D
appears to be off by one).</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-num_branches"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>num_branches</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
number of branches in the morphology. A branch is defined as the
section between soma and bifurcation, between bifurcations, and
between bifurcation and tips. A trifurcation is treated as two
successive bifurcations, so is itself counted as a branch, albeit a
potentially very short one.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_num_branches(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">matches
V3D</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-num_tips"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>num_tips</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
number of terminations (i.e., nodes with zero children) that exist in
the morphology.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_num_branches(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">matches
V3D</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-width"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>width</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
difference between minimum and maximum X position values of all
non-soma nodes in the morphology. Note: This does not implement the
"95%" rule eluded to in the L-measure description.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_dimensions(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">matches
V3D</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-height"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>height</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
difference between minimum and maximum Y position values of all
non-soma nodes in the morphology. Note: This does not implement the
"95%" rule eluded to in the L-measure description.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_dimensions(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">matches
V3D</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-depth"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>depth</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
difference between minimum and maximum Z position values of all
non-soma nodes in the morphology. Note: This does not implement the
"95%" rule eluded to in the L-measure description.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_dimensions(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">matches
V3D</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-max_branch_order"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>max_branch_order</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
maximum number of bifurcations (or trifurcations) encountered between
the soma and all neurite tips (terminations). Branching at the soma
(ie, soma stems) is excluded from the calculation.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_max_branch_order(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Discrepancy
w/ V3D. Using L-Measure definition of branch order, manual
examination of SWC shows max branch order=3 while V3D reports
order=4. V3D appears to include soma stems in calculation, which is
incorrect according to l-measure definition (soma defined as
branch-order=0).</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-mean_contraction"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>mean_contraction</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
ratio of the summed euclidean distance between bifurcations, and
between bifurcations and tips, to the summed path distance between
same. Trifurcations are treated as bifurcations.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_mean_contraction(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Different
than V3D (~1.5%). V3D number closer to the average euclidean distance
over path distance calculated for each bif-bif or bif-tip separately
(V3D has 0.3% difference to that number)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-total_length"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>total_length</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#000000"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
total length of all compartments of a given SWC type.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#000000"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_total_length(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Different
than V3D (off by approx #stems times soma radius). V3D includes
distance from stem base to soma center for each stem. New algorithm
measures length from start of each stem.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-num_neurites"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>num_neurites</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Number
of compartments of a given SWC type.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#000000"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: calculate_num_neurites(morph)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal"><no
V3D correlate></span></span></span></font></font></font></span></em></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-num_nodes"></a>
<em><strong><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>num_nodes</b></span></span></font></font></font></span></strong></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Number
of nodes of a given SWC type</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#000000"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">API
function: Morphology.num_nodes</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Different
than V3D. V3D returns the number of nodes in the SWC file. The new
algorithm returns the number of nodes of a given SWC type (e.g.,
axon, basal dendrite, etc).</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-parent_daughter_ratio"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>parent_daughter_ratio</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Average
ratio of parent to daughter radius for all bifurcations.
Specifically, this is the ratio of each branching node's radius (a
node with >1 child) to each of its children's radius is
calculated, and the average of all of these values is returned.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Different
than V3D (~20%). Reason unknown.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-mean_fragmentation"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>mean_fragmentation</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Fragmentation
is the number of compartments between branch point and branch point,
or branch point and tip (call this a "non-soma segment").
Mean fragmentation is the average of this value for all branch
points. Specifically, the number of compartments in all non-soma
segments is summed, and this is divided by the number of non-soma
segments.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><font color="#993300">Different
than V3D (~10%). Reason as yet unknown. Suspect V3D counts soma as
bifurcation. L-Measure defines fragmentatino based on branch points
(bif-bif and bif-tip). Manual count of</font>compartments and
branches match with new library</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-bifurcation_angle_local"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>bifurcation_angle_local</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
mean angle between child compartments at all bifurcations.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Different
than V3D (~1%). Reason unknown. Manual examination of bifurcations
gives quantitative match to new library</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-bifurcation_angle_remote"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>bifurcation_angle_remote</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#000000"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
mean angle between the next bifurcation or neurite tip as measured at
each bifurcation.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Different
than V3D (~1%). Reason unknown. Manual examination of bifurcations
gives quantitative match to new library</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-soma_surface"></a>
<em><span style="font-variant: normal"><font color="#000000"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>soma_surface</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#000000"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
approximate area of the soma surface. This is 4 * PI * radius^2.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Matches
V3D</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-average_diameter"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>average_diameter</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
average diameter of all non-soma nodes.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Matches
V3D</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-total_surface"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>total_surface</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Total
surface area of all non-soma compartments. This is the sum of 2 * PI
* radius for all non-soma compartments in the morphology.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Different
than V3D. Difference appears to come from V3D calculating the surface
of the soma, and the surface of each soma stem (ie, from soma node to
the first dendrite node)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-total_volume"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>total_volume</b></span></span></font></font></font></span></em></h5>
<p align="left" style="margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1"><a name="MathJax-Element-6-Frame"></a><a name="MathJax-Span-131"></a><a name="MathJax-Span-132"></a><a name="MathJax-Span-133"></a><a name="MathJax-Span-134"></a><a name="MathJax-Span-135"></a><a name="MathJax-Span-136"></a><a name="MathJax-Span-137"></a><a name="MathJax-Span-138"></a><a name="MathJax-Span-139"></a><a name="MathJax-Span-140"></a><a name="MathJax-Span-141"></a><a name="MathJax-Span-142"></a><a name="MathJax-Span-143"></a><a name="MathJax-Span-144"></a><a name="MathJax-Span-145"></a><a name="MathJax-Span-146"></a><a name="MathJax-Span-147"></a><a name="MathJax-Span-148"></a><a name="MathJax-Span-149"></a><a name="MathJax-Span-150"></a><a name="MathJax-Span-151"></a><a name="MathJax-Span-152"></a><a name="MathJax-Span-153"></a><a name="MathJax-Span-154"></a><a name="MathJax-Span-155"></a><a name="MathJax-Span-156"></a><a name="MathJax-Span-157"></a><a name="MathJax-Span-158"></a><a name="MathJax-Span-159"></a><a name="MathJax-Span-160"></a><a name="MathJax-Span-161"></a><a name="MathJax-Span-162"></a><a name="MathJax-Span-163"></a><a name="MathJax-Span-164"></a>
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
sum of <span style="display: inline-block; border: none; padding: 0in"><span style="text-decoration: none"><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i>π</i></font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="3" style="font-size: 12pt">(</font></font></span><span style="text-decoration: none"><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i>Lr</i></font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="2" style="font-size: 9pt">21</font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="3" style="font-size: 12pt">+</font></font></span><span style="text-decoration: none"><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i>L</i></font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="3" style="font-size: 12pt">(</font></font></span><span style="text-decoration: none"><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i>r</i></font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="2" style="font-size: 9pt">2</font></font></span><span style="text-decoration: none"><font size="3" style="font-size: 12pt">−</font></span><span style="text-decoration: none"><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i>r</i></font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="2" style="font-size: 9pt">1</font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="3" style="font-size: 12pt">)+</font></font></span><span style="text-decoration: none"><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i>L</i></font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="3" style="font-size: 12pt">(</font></font></span><span style="text-decoration: none"><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i>r</i></font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="2" style="font-size: 9pt">2</font></font></span><span style="text-decoration: none"><font size="3" style="font-size: 12pt">−</font></span><span style="text-decoration: none"><font face="MathJax Math"><font size="3" style="font-size: 12pt"><i>r</i></font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="2" style="font-size: 9pt">1</font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="3" style="font-size: 12pt">)</font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="2" style="font-size: 9pt">2</font></font></span><span style="text-decoration: none"><font face="MathJax Main"><font size="3" style="font-size: 12pt">)</span></font></font></span> for
all compartments, where L is the length of the compartment and r1,r2
are the radii at each end of the compartment.</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#993300"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Different
than V3D. Half of difference possibly explained by V3D inclusion of
axon segments. Remaining half possibly explained by inclusion of stem
compartments (ie, compartments from soma center to dendrite start)</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h3 class="western" style="margin-top: 0.31in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; line-height: 150%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-Derivedfeatures"></a>
<font color="#333333"><font face="Arial, sans-serif"><font size="3" style="font-size: 12pt"><b>Derived
features</b></font></font></font></h3>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-neurites_over_branches"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>neurites_over_branches</b></span></span></font></font></font></span></em></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#ff0000"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Highly
correlated or equivalent to fragmentation?</font></font></font></p>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">num_neurites</span></span></span></font></font></font></span></em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal"> / </span></span></span></font></font></font></span><em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">num_branches</span></span></span></font></font></font></span></em></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-bifurcation_centroid_over_distance"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>bifurcation_centroid_over_distance</b></span></span></font></font></font></span></em></h5>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_bifurcation_moment_x
/ width</span></span></span></font></font></font></span></em></p>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_bifurcation_moment_y
/ height</span></span></span></font></font></font></span></em></p>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_bifurcation_moment_z
/ depth</span></span></span></font></font></font></span></em></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-compartment_centroid_over_distance"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>compartment_centroid_over_distance</b></span></span></font></font></font></span></em></h5>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_compartment_moment_x
/ width</span></span></span></font></font></font></span></em></p>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_compartment_moment_y
/ height</span></span></span></font></font></font></span></em></p>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_compartment_moment_z
/ depth</span></span></span></font></font></font></span></em></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-bifurcation_variance_over_distance"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>bifurcation_variance_over_distance</b></span></span></font></font></font></span></em></h5>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">second_bifurcation_moment_x
/ width</span></span></span></font></font></font></span></em></p>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">second_bifurcation_moment_y
/ height</span></span></span></font></font></font></span></em></p>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">second_bifurcation_moment_z
/ depth</span></span></span></font></font></font></span></em></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-compartment_variance_over_distance"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>compartment_variance_over_distance</b></span></span></font></font></font></span></em></h5>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">second_compartment_moment_x
/ width</span></span></span></font></font></font></span></em></p>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">second_compartment_moment_y
/ height</span></span></span></font></font></font></span></em></p>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">second_compartment_moment_z
/ depth</span></span></span></font></font></font></span></em></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-bifurcation_centroid_over_stdev"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>bifurcation_centroid_over_stdev</b></span></span></font></font></font></span></em></h5>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_bifurcation_moment</span></span></span></font></font></font></span></em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal"> / </span></span></span></font></font></font></span><strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">sqrt</span></span></span></font></font></font></span></strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">(</span></span></span></font></font></font></span><em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">second_bifurcation_moment</span></span></span></font></font></font></span></em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">)</span></span></span></font></font></font></span></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-compartment_centroid_over_stdev"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>compartment_centroid_over_stdev</b></span></span></font></font></font></span></em></h5>
<p style="margin-left: 0.31in; margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">first_compartment_moment</span></span></span></font></font></font></span></em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal"> / </span></span></span></font></font></font></span><strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">sqrt</span></span></span></font></font></font></span></strong><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">(</span></span></span></font></font></font></span><em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">second_compartment_moment</span></span></span></font></font></font></span></em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">)</span></span></span></font></font></font></span></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<h3 class="western" style="margin-top: 0.31in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; line-height: 150%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-Newfeatures"></a>
<font color="#333333"><font face="Arial, sans-serif"><font size="3" style="font-size: 12pt"><b>New
features</b></font></font></font></h3>
<h5 class="western" style="margin-top: 0.21in; margin-bottom: 0in; border: none; padding: 0in; line-height: 166%; orphans: 1"><a name="Designdocument:morphologycomponentofSDK-num_outer_bifurcations"></a>
<em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b>num_outer_bifurcations</b></span></span></font></font></font></span></em><span style="font-variant: normal"><font color="#707070"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><b> </b></span></span></font></font></font></span></h5>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">Number
of bifurcations (branch points) that exist in the outer region of a
tree or trees. To calculate this, define a sphere with the soma at
center that has a radius of the node furthest from the soma. Define a
second sphere with the center at the soma that has half the radius of
the first sphere. Num_outer_bifs is the number of bifurcations in the
first sphere that are not in the second (ie, the number of
bifurcations that lie outside the second sphere).</font></font></font></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<br/>
</p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; line-height: 0.21in; orphans: 1">
<em><span style="font-variant: normal"><font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt"><span style="letter-spacing: normal"><span style="font-style: normal"><span style="font-weight: normal">early_branch</span></span></span></font></font></font></span></em></p>
<p style="margin-top: 0.1in; margin-bottom: 0in; border: none; padding: 0in; font-variant: normal; letter-spacing: normal; font-style: normal; font-weight: normal; line-height: 0.21in; orphans: 1">
<font color="#333333"><font face="Arial, sans-serif"><font size="2" style="font-size: 10pt">The
ratio of the largest 'short branch' length to the maximum path
length. A short branch is the smaller of branches, as measured by max
path length, coming from a single bifurcation point. Values near 1.0
occur when a stem branches near the soma and both branches from that
bifurcation point are of similar max path length.</font></font></font></p>
<p style="margin-bottom: 0in; line-height: 100%"><br/>
</p>
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