Unit System Reference

This document describes the unit systems used when specifying parameters in BMTK/bionetlite and the unit conversions performed internally.

User-Specified Units (BMTK/bionetlite)

These are the units for parameters specified when building networks with bionetlite. They are the same unit system as BMTK.

Simulation Parameters

Parameter

Unit

Description

Example

tstop

ms

Simulation end time

3000.0

dt

ms

Time step

0.1

v_init

mV

Initial membrane potential

-70.0

Current Injection Parameters

Parameter

Unit

Description

Example

amp

pA

Current injection amplitude

100.0

delay

ms

Current injection start time

500.0

duration

ms

Current injection duration

1000.0

Note

BMTK specifies current in pA units. See BMTK Current Clamps for details.

Synapse Parameters

Parameter

Unit

Description

Example

syn_weight

μS

Synaptic weight

0.001

delay

ms

Synaptic delay

2.0

tau_rise (tau1)

ms

Rise time constant

0.1

tau_decay (tau2)

ms

Decay time constant

1.7

erev (e)

mV

Reversal potential

0.0

Morphology and Ion Channel Files

SWC files and ion channel JSON files are written in the NEURON unit system.

Parameter

Unit

Description

Coordinates (x, y, z)

μm

3D coordinates in SWC file

Radius (r)

μm

7th column of SWC file (radius, not diameter)

Cm

μF/cm²

Membrane capacitance

Ra

Ω·cm

Axial resistance

g_pas (leak)

S/cm²

Leak conductance

Ion channels

S/cm²

Conductance for each channel

Unit Conversions in Internal Processing

For reference, here is a list of unit conversions between NEURON default units and Neulite. The units in the NEURON column are the default unit system based on the NEURON Units Guide.

Unit System List

Category

Variable

NEURON

BMTK

Neulite

Conversion

Conversion Location

Notes

Time

t

ms

ms

ms

None

-

NEURON Unit Chart

Voltage

v

mV

mV

mV

None

-

NEURON Unit Chart

Current (distributed)

i

mA/cm²

mA/cm²

mA/cm²

Yes

ion.c (×10⁻³)

NEURON Unit Chart

Current (point process)

i

nA

pA

nA

Yes

solver.c (×10⁻³)

BMTK Current Clamps

Concentration

ko, ki

mM

mM

mM

None

-

NEURON Unit Chart

Specific capacitance

Cm

μF/cm²

μF/cm²

μF/cm²

None

popl_func.h (area conversion only)

NEURON Unit Chart

Length

L

μm

μm

cm

Yes

popl_func.h (×10⁻⁴)

SWC coordinates are in μm (SWC Spec)

Diameter

diam

μm

μm

cm

Yes

popl_func.h (×10⁻⁴)

SWC 7th column is radius (SWC Spec)

Conductance (distributed)

g

S/cm²

S/cm²

mS/cm²

Yes

popl_func.h (×10³)

NEURON Unit Chart

Conductance (point process)

g

μS

μS

μS

None

-

NEURON Unit Chart

Cytoplasmic resistivity

Ra

Ω·cm

Ω·cm

kΩ·cm

Yes

popl_func.h (×10⁻³)

NEURON Unit Chart

Resistance

Ri()

10⁶ Ω

10⁶ Ω

10⁶ Ω

None

Stored internally in the kernel

NEURON Unit Chart

Other Parameters

Category

NEURON/BMTK

Neulite

Conversion

Conversion Location

Source

DEPTH

μm

cm

Yes

ion_func.h (×10⁻⁴)

NMODL Transpiler

syn_weight

μS

mS

Yes

solver.c (×10⁻³)

SONATA Developer Guide

Conversion from BMTK to NEURON

BMTK converts some parameters to NEURON unit system before passing them.

Parameter

BMTK Input

NEURON Internal

Notes

Current (point process)

pA

nA

BMTK Current Clamps

Developer Information

Conversion Implementation Locations

bionetlite (Python)

bionetlite does not perform unit conversions; the Neulite kernel handles all unit conversions. bionetlite only performs format conversions (JSON→CSV, etc.) and outputs values as-is.

  • convert_ion_channels(): Ion channel JSON → CSV format conversion (values unchanged)

  • convert_morphologies(): SWC file preprocessing (index conversion, axon correction, DFS sorting)

Neulite Kernel (C)

Unit conversions are performed in the Neulite kernel:

  • popl_func.h: Length (μm→cm), Diameter (μm→cm), Ra (Ω·cm→kΩ·cm), Conductance (S→mS)

  • ion_func.h: DEPTH (defined as constant 0.1μm=0.1e-4cm)

  • ion.c: Conversion during ion current calculation (×10⁻³)

  • solver.c: External current i_ext (pA→nA, ×10⁻³), syn_weight (μS→mS, ×10⁻³)

Reference Links