Fiberphotometry Analysis Routies

Basic routines for reading, visualizing and analyzing fiberphotometry recordings.

Local Installation via Anaconda Using a CLI tools (e.g. Anaconda Prompt)

1. install Anaconda.

2. clone the repository:

   git clone https://github.com/GergelyTuri/fiberphotometry.git

   Alternatively, you can download only the environment.yaml file.

3. change directories

   cd fiberphotometry

4. Create a new environment by running the following lines in the anaconda terminal

   conda env create -f environment.yaml

5. activte the environment:

   conda activate fiber-photometry-analysis

6. finally:

   pip install .

   or if you want to install the package in editable mode:

   pip install -e .

Local installation via pip (some sort of environment is higly recommended)

1. clone the repository:

   git clone https://github.com/GergelyTuri/fiberphotometry.git

2. change directories

   cd fiberphotometry

3. finally:

   pip install .

   or if you want to install the package in editable mode:

   pip install -e .

Usage

1. The package can be used as a module in python scripts or jupyter notebooks. E.g.:

import src.fiberphotometry as fp

Installation in a Google Colab notebook

1. open a Colab notebook then type this in a code cell:

   !git clone https://github.com/GergelyTuri/fiberphotometry.git
   %cd fiberphotometry
   !pip install .

2. you may need to restart your runtime/session after this.

Requirements

see environment.yaml or pyproject.toml files for the list of required packages.