read.neuron.swc

read.ngraph.swc

<code>read.neuron.swc</code> reads an SWC file on disk into a fully 
 parsed <code>neuron</code> representation.
<code>read.ngraph.swc</code> reads an SWC file on disk into the more 
 generic (and forgiving) <code>ngraph</code> representation which provides
 a bridge to the <code><a href="/link/igraph?package=nat&version=1.8.24" data-mini-rdoc="nat::igraph">igraph</a></code> library.

NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).

Gregory Jefferis

NeuroAnatomy Toolbox for Analysis of 3D Image Data

James Manton

Dominik Krzeminski

read.neuron.swc function

<dl><dt>f</dt>
<dd>path to file</dd>
<dt>...</dt>
<dd>Additional arguments. <code>read.neuron.swc</code> passes theseto 
<code>as.neuron</code> and then on to <code>neuron</code>. 
<code>read.neuron.swc</code> passes them to <code>ngraph</code>.</dd>
<dt>weights</dt>
<dd>Logical value indicating whether edge weights defined by the 
3D distance between points should be added to graph (default <code>FALSE</code>) 
or a numeric vector of weights.</dd>
<dt>directed</dt>
<dd>Whether the resultant graph should be directed (default TRUE)</dd></dl>

Arguments

According to 
 <a href="http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html">http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html</a> SWC file format has a
 radius not a diameter specification

SWC Format

<code>read.neuron.swc</code> reads an SWC file on disk into a fully 
 parsed <code>neuron</code> representation.
<code>read.ngraph.swc</code> reads an SWC file on disk into the more 
 generic (and forgiving) <code>ngraph</code> representation which provides
 a bridge to the <code><a href='https://rdrr.io/pkg/igraph/man/aaa-igraph-package.html'>igraph</a></code> library.

Read a neuron in swc file format — read.neuron.swc

<dl>

<dt>f</dt>
<dd>path to file</dd>


<dt>...</dt>
<dd>Additional arguments. <code>read.neuron.swc</code> passes theseto 
<code>as.neuron</code> and then on to <code>neuron</code>. 
<code>read.neuron.swc</code> passes them to <code>ngraph</code>.</dd>


<dt>weights</dt>
<dd>Logical value indicating whether edge weights defined by the 
3D distance between points should be added to graph (default <code>FALSE</code>) 
or a numeric vector of weights.</dd>


<dt>directed</dt>
<dd>Whether the resultant graph should be directed (default TRUE)</dd>

</dl>

According to 
 <a href='http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html'>http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html</a> SWC file format has a
 radius not a diameter specification

read.neuron.swc: Read a neuron in swc file format

Description

Usage

Arguments

SWC Format

Details

See Also