itisfoundation / jupyter-pysonic

Jupyter PySONIC

This repository packages PySONIC and MorphoSONIC in a JupyterLab-based Service on o²S²PARC.

JupyterLab with PySONIC and MorphoSONIC for simulation of ultrasound neurostimulation, authored by Théo Lemaire.

Kernels

A Python kernel, with PySONIC, MorphoSONIC and their dependencies (e.g. the NEURON simulator) is installed

Information for developers

Building the docker image:

make build

Test the built image locally:

make run-local

Note that the validation directory will be mounted inside the service.

Raising the version can be achieved via one for three methods. The major,minor or patch can be bumped, for example:

make version-patch

If you already have a local copy of o²S²PARC running and wish to push data to the local registry:

make publish-local

Citation

If this code base contributes to a project that leads to a scientific publication, please acknowledge this fact by citing:

• Lemaire, T., Neufeld, E., Kuster, N., and Micera, S. (2019). Understanding ultrasound neuromodulation using a computationally efficient and interpretable model of intramembrane cavitation. J. Neural Eng. DOI
• Lemaire, T., Vicari E., Neufeld, E., Kuster, N., and Micera, S. (2021). MorphoSONIC: a morphologically structured intramembrane cavitation model reveals fiber-specific neuromodulation by ultrasound. iScience DOI

Testing

In a Jupyter notebook or terminal, run some of the code from the MorphoSONIC repository

Changelog

[2.0.0] - 2023-12-22

• New dynamics-sidecar version, from original version in GitLab
• Added MorphoSONIC