Discretization

Before Arbor can actually simulate the behavior of a cell using the interplay of morpholgy, mechanisms, etc it needs to turn the contiguous morphology into a collection of discrete, conical sub-volumes. These are called ‘compartments’ or ‘control volumes’ (CV). The granularity of the subdivision controls the precision of the simulation and its computational cost. We describe the expression syntax and API methods below.

Arbor offers a set of composable discretization policies

(cv-policy-explicit locset region)

Use the subdivision as given by locset

API

  • cv_policy_explicit(locset)

(cv-policy-max-extent ext region flags)

Subdivision into CVs of at most ext \(\mu m\). In the vicinity of fork points, smaller CVs might be used to avoid producing CVs containing forks, unless flags is (flag-interior-forks).

API

  • cv_policy_max_extent_um(length_um, region=all(), flags=none), length in \(\mu m\)

  • cv_policy_max_extent(quantity, region=all(), flags=none), length will be converted from conforming quantity

(cv-policy-fixed-per-branch count region flags)

Subdivide each branch into count equal CVs. In the vicinity of fork points, smaller CVs might be used to avoid producing CVs containing forks, unless flags is (flag-interior-forks).

API

  • cv_policy_fixed_per_branch(count, region=all(), flags=none)

(cv-policy-every-segment region)

Each segment — as given during morphology construction — will produce one CV.

API

  • cv_policy_every_segment(region=all())

(cv-policy-default) = (cv-policy-fixed-per-branch 1)

Each branch will produce one CV.

API

  • default_cv_policy()

(cv-policy-single region)

The whole region will produce one CV.

API

  • cv_policy_single(region=all())

In all cases region is optional and defaults to (all), i.e. the whole cell. These policies compose through

(join cvp1 cvp2)

Use the union of the boundary points defined by cvp1 and cvp2.

API

  • cvp1 + cvp2

(replace cvp1 cvp2)

Use the boundary points defined by cvp1 everywhere except where cvp2 is defined. There, use those of cvp2.

API

  • cvp1 | cvp2