NeuroChaT v1.2.0

NeuroChaT (RRID:SCR_018020) is an open-source neuron characterisation toolbox. It is described in our paper on Wellcome Open Research.

Author Contributions

Md Nurul Islam, Sean K. Martin, Shane M. O'Mara, and John P. Aggleton.

MNI: Original conception and design of the software architecture, primary development of algorithms and subsequent implementation in Python, primary user's manual development, iterative development of software based on user feedback, originator of NeuroChaT acronym.

MNI, SKM: Developing analysis algorithms, MATLAB/Python script writing and validation, analysis and interpretation of data.

SKM: Additional Python routines for LFP and place cell analysis, NeuroChaT API examples, recursive batch analysis, software testing.

SMOM: Original conception and statement of software need, project guidance and feedback.

JPA, SMOM: Grant-fundraising, analysis and interpretation of data.

Acknowledgments

This work was supported by a Joint Senior Investigator Award made by The Wellcome Trust to JP Aggleton and SM O'Mara. We thank Paul Wynne, Pawel Matulewicz, Beth Frost, Chris Dillingham, Katharina Ulrich, Emanuela Rizzello, Johannes Passecker, Matheus Cafalchio and Maciej Jankowski for comments and feedback on the various iterations of NeuroChaT.

Installation

If you are on Windows, it is possible to use a Graphical version of neurochat, that can be downloaded as a single executable file. Otherwise, Python version 3.5 upwards is required to install neurochat. Installation steps are listed in detail below:

Option 1: Use Pip

Open command prompt and type/paste the following. It is recommended to install neurochat to a virtual environment (E.g. using virtualenv), if doing so, activate it before typing these commands.

git clone https://github.com/seankmartin/NeuroChaT
cd NeuroChaT
pip install .
python cli.py

Option 2: Use Docker

This option is aimed towards Linux users, and is not tested on Windows. Firstly, install Docker, and then run the following in command prompt:

docker pull seankmartin/neurochat
xhost local:root
export QT_X11_NO_MITSHM=1
docker run --volume /tmp/.X11-unix:/tmp/.X11-unix --env DISPLAY=unix$DISPLAY --name=neurochat seankmartin/neurochat

To access your host data in the Docker container, mount the data in the run command, like so

docker run --mount type=bind,source=/home/username/my-data,target=/mnt/my-data --volume /tmp/.X11-unix:/tmp/.X11-unix --env DISPLAY=unix$DISPLAY --name=neurochat seankmartin/neurochat

To build a docker image of the master branch, instead of running docker pull, run the below command, and replace seankmartin/neurochat by neurochat:master

git clone https://github.com/seankmartin/NeuroChaT
cd NeuroChaT
docker build -t neurochat:master .

Option 3: Use Pip, but don't install NeuroChaT

Open command prompt and type/paste the following.

git clone https://github.com/seankmartin/NeuroChaT
cd NeuroChaT
pip install -r requirements.txt
python modify_neuro_path.py
python cli.py

This method only allows the GUI program to function, any other file will need to modify the python path to use neurochat.

Option 4: Use conda

It is also possible to install NeuroChaT into a conda (Anaconda) environment

git clone https://github.com/seankmartin/NeuroChaT
cd NeuroChaT
conda create -f environment.yml
pip install .
python cli.py

Install PyQt5 on linux

If you are running NeuroChaT GUI on linux, after installing the requirements you will need to install further qt programs. Most likely, you only need python3-pyqt5, but just in case it might be safest to install all three of these if you have the available disk space.

sudo apt-get install python3-pyqt5
sudo apt-get install pyqt5-dev-tools
sudo apt-get install qttools5-dev-tools

Getting Started

The best ways to get started with NeuroChaT are:

1. For using the UI, download the executable file for Windows and check out the user manual.
2. For using the Python Code, checkout the nice notebook made by Md Nurul Islam, a repository containing a set of scripts using NeuroChat by Sean Martin, and examples in this repository.

We are open to collaborators, questions, etc. so feel free to get in touch!

Documentation

See our Read the docs website for documentation and examples.

Open Science Framework Storage

Sample hdf5 datasets and results are stored on OSF, at https://osf.io/kqz8b/files/.

Version

The NeuroChaT version number should be maintained in:

1. setup.py
2. neurochat\__init__.py
3. README.md

Troubleshooting

If you are trying to run NeuroChaT from Python source code, and are having problems, the first port of call should be to install the requirements from fixed_requirements.txt instead of the normal source.

Current known bugs

1. From the GUI, if an LFP file is analysed, and then a subsequent LFP file is attempted to be loaded but fails - the program returns the results for the first LFP file analysed. This should be a relatively simple fix. This may only happen for 0 length LFP files, but needs further testing.
2. Loading a config file with mode set to 2 fails to correctly load the excel file, but loads the parameters correctly.