dendra-models 0.2.0

Reference neuronal cell and network models implemented with Dendra.

Documentation · Source · Issue tracker · PyPI

Installation

Dendra Models requires Python 3.11 or later. Install the released package from PyPI:

python -m pip install dendra-models

This installs Dendra with its solvers extra, including dendra-solvers. On supported platforms, pip uses a prebuilt solver wheel. These native solvers are the default CPU backends for Dendra Models' block and tree models.

For an editable development installation, see CONTRIBUTING.md.

Quick start

Models are available from dendra_models.models:

import dendra as dn
from dendra_models.models import exactMRG

with dn.ctx(DTYPE="float64", DEVICE="cpu", JIT=0):
    model = exactMRG(diameters=[5.7], n_node=3)
    model.eval()
    model.initialize()

Examples

The repository includes focused examples for threshold finding, kilohertz-frequency stimulation, and C-fiber simulations.

Available models

Peripheral nerve fibers

Unmyelinated

Myelinated

MRG and surrogate

Other

Cortical neurons

Myelinated

The packaged cortical morphologies are modified derivatives of Blue Brain Project/EPFL cortical neuron morphologies, rather than unmodified copies. Their axonal arbors were modified and myelinated following the procedures described in:

• Aberra, A.S., Peterchev, A.V., Grill, W.M., 2018. Biophysically realistic neuron models for simulation of cortical stimulation. Journal of Neural Engineering 15, 066023. https://doi.org/10.1088/1741-2552/aadbb1
• Aberra, A.S., Wang, B., Grill, W.M., Peterchev, A.V., 2020. Simulation of transcranial magnetic stimulation in head model with morphologically-realistic cortical neurons. Brain Stimulation 13, 175–189. https://doi.org/10.1016/j.brs.2019.10.002

These morphology files are licensed under CC BY-NC-SA 4.0. See THIRD_PARTY_NOTICES.md for their source, attribution, modifications, and file scope.

Networks

Brain and cortical

Spine

The Zhang 2014 Wind-Up vectors are obtained separately from ModelDB. This is an explicit one-time download; importing Dendra Models and constructing other models never accesses the network:

from dendra_models.models.networks.zhang_2014 import download_windup_data

download_windup_data()

The downloader uses an immutable upstream revision, verifies SHA-256 hashes, and stores the vectors in a revision-specific user cache. Pass data_dir= to load_windup_data() or build_windup_network() to use an existing or modified vector realization instead. See the Wind-Up data notes for the cache location and vector semantics.

License

Dendra Models code and the trained SMF.pt model parameters are distributed under Duke University's custom license for non-commercial research and academic testing. Commercial use, including industrially sponsored research, requires a separate agreement with Duke's Office for Translation and Commercialization. The complete Duke terms are in LICENSE.md.

The cortical morphology files under src/dendra_models/models/cells/cortical/ are separately licensed adapted material under CC BY-NC-SA 4.0. The Duke license does not replace the Creative Commons terms for those files. File-level details and required attribution are in THIRD_PARTY_NOTICES.md.

Contributing and support

See CONTRIBUTING.md to set up a development environment and submit a GitHub pull request. Please report security concerns using the private process in SECURITY.md.