MEArec is a Python package and it can be easily installed using pip:
pip install MEArec
If you want to install from sources and be updated with the latest development you can install with:
git clone https://github.com/alejoe91/MEArec cd MEArec python setup.py install (or develop)
The following are the Python requirements, which are installed when running the pip installer.
Additional requirements for template generatiom¶
The template generation requires the NEURON simulator to be installed. From MEArec version 1.7.0, NEURON version 7.8 is supported. On UNIX systems NEURON can be installed with:
pip install neuron
On Windows machines, NEURON can be downloaded and installed from this link.
LFPy is used to generate extracellular templates. It is not installed by default, but it can be easily installed with:
pip install LFPy>=2.2
Test the installation¶
You can test that MEArec is correctly imported in python:
import MEArec as mr
And that the CLI is working. Open a terminal and run:
You should get the list of available commands:
Usage: mearec [OPTIONS] COMMAND [ARGS]... MEArec: Fast and customizable simulation of extracellular recordings on Multi-Electrode-Arrays Options: --help Show this message and exit. Commands: available-probes Print available probes. default-config Print default configurations. gen-recordings Generates RECORDINGS from TEMPLATES. gen-templates Generates TEMPLATES with biophysical simulation. set-cell-models-folder Set default cell_models folder. set-recordings-folder Set default recordings output folder. set-recordings-params Set default templates output folder. set-templates-folder Set default templates output folder. set-templates-params Set default templates output folder.