MaxSim

Overview

This is a format used by the MaxSim[1] axonal simulator software

Format specification:

Encoding:  ASCII text
Limitations: No soma, no dendrite data. No spines. No markers.

The first line takes the form

# number of nodes: XXX

where XXX is the total number of sample points included in the data.

Subsequent lines which begin with a '#' denote the start of a new structure.  These take the form

# <structure_name>:  <structure_number>  <structure_start_node>

where <structure_name>  is  'pia_line', 'axon', or 'white_matter_line'.  The relevant node data follows directly after this line.

Other non-empty lines each represent a single sample point, using eight or nine data items.


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data type
 Node number
 Node Type
 Parent Node
 Daughter  Node 1
 Daughter Node 2
 x position
 y position
 z position
 diameter
data value
 contiguous, starting from '0'
 '0' - structure start point
'1' - bifurcation point
'2' - continuous point
'4' - other
 The node number of the  parent node.
'-1' if the node has no parent.


 The node number of the first daughter node.
'-1'  if there are no daughters, i.e. terminal branch.
Otherwise (branchpoint or continuous point), numbering is continuous from the parent node.
 The start node number of the second daughter branch (parent)
'-1'  if there are no daughter nodes, i.e. when this node represents a terminal point or continous point.
 'x', 'y', 'z' are spatial co-ordinates, given in micrometers.
'diameter' is dendrite thickness, also given in micrometers.  Diameter is omitted for non-axon data, and for axon bifurcation points.


References

[1]  Tettoni L, Lehmann P, Houzel J-C, Innocenti GM (1996) Maxsim, software for the analysis of multiple axonal arbors and their simulated activation. J Neurosci Methods 67: 1–9.


Links

There no longer seems to be any working links to the original documentation. (Please provide a link if you know of one!!)

Examples

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