ind2coord

ind2coord.default

ind2coord.array

ind2coord.im3d

If you have an image-like object and you want to turn it into a 
 matrix of 3D coords then you need <code>ind2coord</code>. For the reverse
 operation we offer <code>as.im3d.matrix</code> which allows you to turn a
 matrix of 3D coordinates into an <code>im3d</code> image object.

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

ind2coord function

<dl><dt>inds</dt>
<dd>indices into an image array (either 1D, for which <code>dims</code> 
must be present, or a logical array).</dd>
<dt>...</dt>
<dd>extra arguments passed to methods.</dd>
<dt>dims</dt>
<dd>dimensions of 3D image array.</dd>
<dt>voxdims</dt>
<dd>vector of 3 voxel dimensions (width, height, depth).</dd>
<dt>origin</dt>
<dd>the origin.</dd></dl>

Arguments

Find XYZ coords corresponding to 1D indices into a 3D image — ind2coord

<dl>

<dt>inds</dt>
<dd>indices into an image array (either 1D, for which <code>dims</code> 
must be present, or a logical array).</dd>


<dt>...</dt>
<dd>extra arguments passed to methods.</dd>


<dt>dims</dt>
<dd>dimensions of 3D image array.</dd>


<dt>voxdims</dt>
<dd>vector of 3 voxel dimensions (width, height, depth).</dd>


<dt>origin</dt>
<dd>the origin.</dd>

</dl>

ind2coord: Find XYZ coords corresponding to 1D indices into a 3D image

Description

Usage

Arguments

See Also