Introduction

Purpose

xcell aims to provide a simple toolkit for simulating the extracellular space, in conjunction with an intracellular model such as NEURON. In particular, it’s geared toward dynamically adaptive meshing, making larger simulations more computationally manageable.

At present, the software is at an early alpha stage; some modifications may be needed to get it working on your machine. The gallery examples give an idea of the functionality baked into the library and how to use it; detailed documentation of the API is also available.

Installing

To minimize the chance of compatibility issues (and take advantage of much faster installers), it’s best to use the Mambaforge distribution instead of a standard Anaconda distribution, though that should be possible as well (using conda in place of mamba. MacOS and Windows installations are not yet fully tested, but no further steps beyond this guide should be needed for Linux.

In the directory where you download xcell, create an environment by executing

mamba env create -f xcell

Follow the installation instructions for NEURON according to your operating system.

Finally, install xcell (in developer mode) with

pip install -e .

(the -e flag can be omitted if you don’t want to modify xcell’s own code)

Citation

coming soon