find.soma

Find neurons with soma inside 3D selection box (usually drawn in rgl window)

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

find.soma function

<dl><dt>sel3dfun</dt>
<dd>A <code>select3d</code> style function to indicate if points
are within region</dd>
<dt>indices</dt>
<dd>Names of neurons to search (defaults to all neurons in list)</dd>
<dt>db</dt>
<dd><code>neuronlist</code> to search. Can also be a character vector naming 
the neuronlist. Defaults to <code>options('nat.default.neuronlist')</code>.</dd>
<dt>invert</dt>
<dd>Whether to return neurons outside the selection box (default 
<code>FALSE</code>)</dd>
<dt>rval</dt>
<dd>What to return (character vector, default='names')</dd></dl>

Arguments

Find neurons with soma inside 3D selection box (usually drawn in rgl window) — find.soma

<dl>

<dt>sel3dfun</dt>
<dd>A <code>select3d</code> style function to indicate if points
are within region</dd>


<dt>indices</dt>
<dd>Names of neurons to search (defaults to all neurons in list)</dd>


<dt>db</dt>
<dd><code>neuronlist</code> to search. Can also be a character vector naming 
the neuronlist. Defaults to <code>options('nat.default.neuronlist')</code>.</dd>


<dt>invert</dt>
<dd>Whether to return neurons outside the selection box (default 
<code>FALSE</code>)</dd>


<dt>rval</dt>
<dd>What to return (character vector, default='names')</dd>

</dl>

find.soma: Find neurons with soma inside 3D selection box (usually drawn in rgl window)

Description

Usage

Value

Arguments

Details

See Also