Regions & Locsets

Regions & Locsets#

When you decorate a multi-compartment cell you must say where a mechanism goes. braincell answers this with two kinds of selection expression, both living in braincell.filter:

  • a region selects an extended set of cable — “the soma”, “all apical dendrites”, “everything within 100 µm of the root”. You paint density mechanisms onto regions.

  • a locset selects a set of points — “the root”, “all branch tips”, “every 50 µm”. You place point mechanisms onto locsets.

import braincell.filter as f

Note

This mirrors the labels idea in simulators like Arbor: a small, composable algebra for naming parts of a morphology, kept separate from the mechanisms you attach to them.

Regions (paint targets)#

Expression

Selects

AllRegion

the entire cell

EmptyRegion

nothing (useful as an identity in set operations)

branch_in()

branches matching a property, e.g. branch_in("type", "soma")

branch_range() / BranchRangeFilter

a sub-interval along branches

SubtreeRegion

a branch and everything distal to it

RadiusRangeRegion

cable whose radius falls in a range

EuclideanDistanceRegion / TreeDistanceRegion

cable within a straight-line / along-the-tree distance

 
from braincell.filter import AllRegion, branch_in

cell.paint(AllRegion(), mech.Channel("IL", g_max=0.0003 * u.S / u.cm**2, E=-70. * u.mV))
cell.paint(branch_in("type", "soma"), mech.Channel("Na_Ba2002", g_max=0.12 * u.S / u.cm**2))
cell.paint(
    branch_in("type", ("dendrite", "basal_dendrite", "apical_dendrite")),
    mech.Channel("CaL_IS2008", g_max=0.002 * u.S / u.cm**2),
)

Locsets (place targets)#

Expression

Selects

RootLocation

a point on the root branch, e.g. RootLocation(0.5) (the midpoint)

Terminals

all terminal tips

BranchPoints

all branch points (bifurcations)

UniformSamples / StepSamples

evenly / step-spaced points along the cell

RandomSamples

randomly sampled points

at() / AtLocation

a specific (branch, position) location

 
from braincell.filter import RootLocation, Terminals

cell.place(RootLocation(0.5), mech.CurrentClamp(durations=50 * u.ms, amplitudes=0.2 * u.nA))
cell.place(Terminals(), mech.StateProbe("V"))

Composing selections#

Both regions and locsets support set operations — union, intersection, difference — so you can build precise targets from simple parts (RegionSetOp, LocsetSetOp, and the mask variants). This is the same composability that makes mechanisms reusable: name a place once, decorate it many times.

braincell.filter also caches selection results (SelectionCache) so repeated paints over the same region don’t recompute the membership.

See also#