normalise_swc

Normalise an SWC format block of neuron morphology data

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

normalise_swc function

<dl><dt>x</dt>
<dd>A data.frame containing neuron morphology data</dd>
<dt>requiredColumns</dt>
<dd>Character vector naming columns we should have</dd>
<dt>ifMissing</dt>
<dd>What to do if <code>x</code> is missing a required column</dd>
<dt>includeExtraCols</dt>
<dd>Whether to include any extra columns included in
<code>x</code></dd>
<dt>defaultValue</dt>
<dd>A list containing default values to use for any missing
columns</dd></dl>

Arguments

Normalise an SWC format block of neuron morphology data — normalise_swc

<dl>

<dt>x</dt>
<dd>A data.frame containing neuron morphology data</dd>


<dt>requiredColumns</dt>
<dd>Character vector naming columns we should have</dd>


<dt>ifMissing</dt>
<dd>What to do if <code>x</code> is missing a required column</dd>


<dt>includeExtraCols</dt>
<dd>Whether to include any extra columns included in
<code>x</code></dd>


<dt>defaultValue</dt>
<dd>A list containing default values to use for any missing
columns</dd>

</dl>

normalise_swc: Normalise an SWC format block of neuron morphology data

Description

Usage

Value

Arguments

Details

See Also