/MEA-analysis

Data science project to analyse a multi-electrodes recording

Primary LanguageJupyter NotebookGNU General Public License v3.0GPL-3.0

Install

Prerequisits

Python 3.5+ or Anaconda3

For windows download and install Visual c++ https://visualstudio.microsoft.com/downloads/

Create environments and install packages

A good practice is creates a virtual environment with conda (or virtualenv) because create a isolated python environment.

$ conda env create -f conda_environment.yml
$ conda activate spklib # if you have problems with it, try windows: activate spklib linux: source activate spklib

or use virtualenv

$ virtualenv --python=python3.7 venv
$ source venv/bin/activate
$ pip install -r requirements.txt
$ pip install -r requirements_git.txt

Download external library to load mcd files

To read mcd files spikelib package use neuroshare package to do it. So you need download the correct .dll (windows) or .so (linux) file. For more details about neuroshare see https://pythonhosted.org/neuroshare/

Download neuroshare lib from https://www.multichannelsystems.com/software/neuroshare-library

For Linux:

$ tar xvzf nsMCDLibrary_Linux64_3.7b.tar.gz
$ cp nsMCDLibrary/* ~/.neuroshare/

For Windows:

1) UNCOMPRESS nsMCDLibrary_3.7b.zip file 
2) COPY nsMCDLibrary_3.7b\Matlab\Matlab-Import-Filter\Matlab_Interface\nsMCDLibrary64.dll
3) PASTE TO your_path\Anaconda3\envs\spklib\DLLs\nsMCDLibrary64.dll
4) RENAME nsMCDLibrary64.dll TO nsMCDLibrary.dll

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