HOC CODE TO COLLAPSE A DENDRITIC TREE
=====================================
Collapse a dendritic tree into 3 compartments "proximal", "middle"
and "distal".
The collapse is made such as the collapsed dendritic structure
preserves the axial resistance of the original structure.
The algorithm works by merging successive pairs of dendritic
branches into an equivalent branch (a branch that preserves the
axial resistance of the two original branches).
This merging of branches can be done according to different methods
selectable in the present code:
AREABYLONG
The code rejects the smallest original branch if it is more than
5 times smaller than the long orginal branch. If AREABYLONG is
set to 1, then the small branch is rescaled to the longest one
(a new diameter is assigned such that the small branch conserves
its axial resistance). This minimizes errors for dendritic
structures where branches have a large range of possible lengths.
AREABYLONG = 0 is the default.
AVGLENGTH, AVGLENGTHWDIAM, AVGLENGTHWSURF
During the merging of two branches, the length of the equivalent
branch is calculated by one out of three possible methods.
First, a simple average of the two branch length:
L = (L1+L2)/2
This is the method originally used by Bush and Sejnowski
(J. Neurosci. Methods 46: 159-166, 1993).
It is selected by setting AVGLENGTH=1.
Second, by weighting this average with the diameters of each branch
L = (diam1*L1 + diam2*L2)/(diam1+diam2)
This algorithm produces more fair merging in the case two branches of
very different diameters are to be merged. It is selected by setting
AVGLENGTHWDIAM=1.
Third, by weighting the average with membrane area:
L = (area1*L1 + area2*L2)/(area1+area2)
This algorithm is better in the case two branches of very different
areas are to be merged. It is selected by setting AVGLENGTHWSURF=1.
CUTOFF1, CUTOFF2
The dendritic branches are assigned to one of the three compartments
("proximal", "middle" or "distal") based on their path axial
resistance (in Meg-Ohms) to the soma. The cutoff values (CUTOFF1
and CUTOFF2) determine these cut-offs. For example, CUTOFF1=10 means
that all branches laying within 10 Meg-Ohm of axial resistance from
the soma will be merged together into the same ("proximal") section.
Written by M. Neubig & A. Destexhe
Laval University, 1997; CNRS 2000
The run this example, enter:
nrniv collapse.hoc -
it should give the following output:
Section Length (um) Diameter (um)
1 70.69612 7.9574464
2 28.123442 8.0002892
3 12.49237 10.281249