compneurovis 0.4.0a1

Interactive visualization toolkit for computational neuroscience simulations and data

CompNeuroVis

CompNeuroVis connects computational neuroscience simulations and data to interactive desktop visualizations. Sources expose model data and controls; views opt into line plots, morphology, surfaces, and other panels; cnv.show() integrates those pieces into one application.

Alpha Status

CompNeuroVis 0.4.0a1 is an alpha release. All versions before 1.0.0 are unstable prereleases. Public APIs may change between releases.

This release supports the inline source workflow used by current examples. Notebook, distributed, and multi-source composition paths remain experimental.

Installation

CompNeuroVis requires Python 3.11.

Install the alpha release:

pip install --pre compneurovis

Install current checkout:

pip install -e .

Install optional simulator integrations:

pip install -e ".[neuron]"
pip install -e ".[jaxley]"

Notebook dependencies are experimental:

pip install -e ".[notebook]"

Minimal App

import math

import compneurovis as cnv


state = {"time_ms": 0.0, "frequency_hz": 1.0}


def step(ctx):
    state["time_ms"] += 16.0


def set_frequency(ctx, value):
    state["frequency_hz"] = float(value)


src = cnv.source(step)

wave = src.line(
    "Sine wave",
    read=lambda: math.sin(
        2.0
        * math.pi
        * state["frequency_hz"]
        * state["time_ms"]
        / 1000.0
    ),
    x=lambda: state["time_ms"],
    y_min=-1.1,
    y_max=1.1,
)

src.slider(
    "frequency_hz",
    label="Frequency (Hz)",
    get=lambda: state["frequency_hz"],
    set=set_frequency,
    min=0.1,
    max=5.0,
)

cnv.layout(((wave,), (src.controls_panel,)))
cnv.show(title="Sine wave")

Run repository version:

python examples/custom/sine_wave.py

NEURON Morphology

NEURON sources keep simulator-specific data collection optimized while using the same line, control, layout, and show API.

from neuron import h

import compneurovis as cnv


soma = h.Section(name="soma")
soma.L = soma.diam = 20.0
soma.insert("hh")

stim = h.IClamp(soma(0.5))
stim.delay = 100.0
stim.dur = 5.0
stim.amp = 0.8


def set_stimulus(ctx, value):
    stim.amp = float(value)


src = cnv.neuron.source(
    sections=[soma],
    dt=0.025,
    display_dt=0.5,
)

morphology = src.morphology(
    variable="v",
    name="Membrane voltage",
    unit="mV",
    color_limits=(-80.0, 50.0),
    selected="soma@0.50000",
)

voltage = src.line(
    "Selected voltage",
    source=morphology.selection,
    variables={"Voltage": "v"},
    y_unit="mV",
    rolling_window=500.0,
)

src.slider(
    "stimulus",
    label="Stimulus amplitude (nA)",
    get=lambda: stim.amp,
    set=set_stimulus,
    min=0.0,
    max=2.0,
)

cnv.layout(((morphology, voltage), (src.controls_panel,)))
cnv.show(title="NEURON morphology")

Full showcase:

python examples/neuron/complete_interface.py

Static surface showcase:

python examples/widgets/surface.py

Supported Alpha Surface

• cnv.source(...) for Python callables, iterators, and static data.
• cnv.neuron.source(...) and cnv.jaxley.source(...) for simulator-native sources.
• Source-level line, bar, morphology, and surface views.
• Typed controls and actions used by current examples.
• cnv.layout(...) for single-app panel placement.
• cnv.show(...) with VisPy and PyQt6 desktop rendering.

Views are opt-in. A simulator source can own morphology without displaying a morphology panel.

Experimental

These paths are incomplete or not release-supported:

• Notebook frontends and notebook process lifecycle.
• Remote sources and remote actors.
• Source composition and independent multi-source execution.
• Multi-source custom layouts.
• Advanced callback access through backend internals.

Incomplete distributed entrypoints live under cnv.experimental so they are not mistaken for supported root-level API.

Documentation

Start with Getting Started, then follow the ordered Example Path.

Build the documentation site locally:

python -m mkdocs build --strict

License

Apache License 2.0.