Pipeline VSDI

Preprocessing tools for voltage sensitive dye imaging data

Structure

• VSDI_Session - Contains classes for handling sessions and full datasets.
• io - Contains data loaders and savers.
• cleaning - Contains functions to clean and handle the data
• embedding - Contains functions to perform linear (PCA-ICA) and nonlinear (convolutional variational autoencoders) dimensionality reduction on the vsdi video data.
• decoding - Contains functions to perform decoding of the behavioural output from the neural activity

Installation

Prerequisites

• Python 3.7 or higher
• Poetry Python packaging and dependency management tool.

Steps

1. Clone the repository

git clone https://github.com/dabadav/pipeline_vsdi.git
cd pipeline_vsdi

2. Install the package using Poetry

Ensure you're in the pipeline_vsdi directory (or the directory where you cloned your repository) and run:

poetry install

This command installs all the dependencies specified in the pyproject.toml file in a new virtual environment. If you want to use the virtual environment for other tasks, you can activate it using:

poetry shell

After this, you should have all the necessary dependencies installed and be able to use the functionality provided by the Pipeline VSDI.

Usage

After installation, you can import and use the tools in the Python interpreter or your scripts like:

from vsdi import Session
from preprocessing import clean_data
from dim_reduction import reduce_dimension

# Use the tools as per your requirement.