ArborVitae

Overview

This is a format used by the ArborVitae software by Senft[1]  (this software does not seem to be publicly available).
This software employs algorithms to generate artificial neuroanatomy data.

Format specification   

The format specification is not available online, therefore the information presented here is derived from publicly available data, and may not be complete.

Encoding:  ASCII text
Limitations: Binary trees only.  Point soma. No markers. No spines.

Lines which begin with a '#' are comments.

Other non-empty lines each represent a single neuron sample point with seven data items (separated by whitespace).

	1	2	3	4	5	6	7
data type	Sample number	Point Type	Object number	x position	y position	z position	diameter
data value	contiguous, starting from '1'	Single character - S - Soma B - Branch C - Continuous T - Terminal P - Primary	An integer	'x', 'y', 'z' are spatial co-ordinates, given in micrometers. 'diameter' is dendrite thickness, also given in micrometers.

Note that sample connectivity is implicit in the data - the data point directy following a terminal point (T) is connected to the first incomplete binary branch point encountered when ascending the tree hierarchy.

References

[1] http://krasnow.gmu.edu/cn3/TNA/index.htm


Links

Online data source -  http://krasnow.gmu.edu/cn3/L-Neuron/database/index.html
L-Neuron -   http://krasnow.gmu.edu/cn3/L-Neuron/index.htm


Examples

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