Groups segments of tree intree together when they belong to the same branch. Can be used as sections in NEURON-like compartmental modelling (see “neuron_tree”). Branches are delimited by either branching or termination points or region-defined borders.

TREES

Output matrix sect of size nx2 where n is the number of branches contains starting and end nodes of each branch. Nx2 matrix vec attributes a branch to each node and a fractional path length along this branch.

(Note that in the example below, nodes 14 and 15 form a separate region called “1”, which reflects in the NEURON code below.)

Example:

>> [sect vec] = dissect_tree (sample2_tree);

>> sect'

1 3 6 6 3_ 10 12 12 10  → starting nodes
3 6 8 9 10 12 13 14 15  → ending nodes

>> vec'

1 1_ 1 2__ 2_ 2 3__ 3 4 5 6__ 6 7 8 9  → segment index
0 .5 1 .35 .7 1 .47 1 1 1 .58 1 1 1 1  → fractional path length

corresponding NEURON connectivity

connect tree_dendrite[1](0), tree_dendrite[0](1)
connect tree_dendrite[2](0), tree_dendrite[1](1)
connect tree_dendrite[3](0), tree_dendrite[1](1)
connect tree_dendrite[4](0), tree_dendrite[0](1)
connect tree_dendrite[5](0), tree_dendrite[4](1)
connect tree_dendrite[6](0), tree_dendrite[5](1)
connect tree_1[0](0), tree_dendrite[5](1)
connect tree_1[1](0), tree_dendrite[4](1)

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