read.neuron.fiji

Read a neuron saved by Fiji's Simple Neurite Tracer Plugin

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.fiji function

<dl><dt>f</dt>
<dd>Path to a file</dd>
<dt>...</dt>
<dd>Additional arguments passed to <code><a href="/link/xmlParse?package=nat&version=1.8.24" data-mini-rdoc="nat::xmlParse">xmlParse</a></code>.</dd>
<dt>simplify</dt>
<dd>Whether to return a single neuron as a <code>neuron</code> object 
rather than a <code>neuronlist</code> of length 1.</dd>
<dt>Verbose</dt>
<dd>Whether to print status messages during parsing.</dd></dl>

Arguments

Read a neuron saved by Fiji's Simple Neurite Tracer Plugin — read.neuron.fiji

<dl>

<dt>f</dt>
<dd>Path to a file</dd>


<dt>...</dt>
<dd>Additional arguments passed to <code><a href='https://rdrr.io/pkg/XML/man/xmlTreeParse.html'>xmlParse</a></code>.</dd>


<dt>simplify</dt>
<dd>Whether to return a single neuron as a <code>neuron</code> object 
rather than a <code>neuronlist</code> of length 1.</dd>


<dt>Verbose</dt>
<dd>Whether to print status messages during parsing.</dd>

</dl>

read.neuron.fiji: Read a neuron saved by Fiji's Simple Neurite Tracer Plugin

Description

Usage

Arguments

Details

References