Antelop

Antelop is a complete data processing and management tool for systems neuroscientists.

It allows you to easily adopt modern data engineering infrastructures and efficient data preprocessing pipelines in a simple graphical application. It also provides a host of visualisation tools and a standard library of common analysis functions, as well as a framework for you to write your own fully reproducable analysis functions.

At present, Antelop supports electrophysiology, calcium imaging, and behavioural data.

To learn more about Antelop, please read our documentation.

Installation

The terminal interface of Antelop can be installed via pip. Note that Antelop requires python 3.9:

pip install antelop

To minimise installation time, a number of features are offered as optional dependencies.

pip install antelop[gui] # For our graphical user interface

pip install antelop[gui, phy] # For electrophysiology manual curation

pip install antelop[gui, dlc] # For deeplabcut subject pose estimation

pip install antelop[full] # For everything (longer installation time)

Conda users can get started as follows:

conda create -n antelop python=3.9
conda activate antelop
pip install antelop

Usage

To run the gui:

antelop

Antelop user interface

You will be prompted for your database login credentials.

To run the IPython console interface:

antelop-python

To use Antelop in a script, set the $DB_USER and $DB_PASS environment variables, then import all the tables and analysis functions as follows:

from antelop.load_connection import *

Authors

Developed by Rory Bedford in the Tripodi Lab.

License

MIT License

Copyright (c) 2024 Rory Bedford

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.