VoDEx: Volumetric Data and Experiment Manager

VoDEx is an open-source Python library that streamlines the management and analysis of volumetric functional imaging data. It offers a suite of tools for creating, organizing, and storing information pertaining to image acquisition and time annotation. Additionally, it allows for the retrieval of image data based on specific experimental conditions, enabling researchers to access and analyze the data easily. VoDEx is available as both a standalone Python package and a napari plugin, providing a user-friendly solution for processing volumetric functional imaging data, even for researchers without extensive programming experience.

Quick Start

To get started with VoDEx, please see Quick Start and Examples.

API Reference

The API contains the technical implementation of the VoDEx project code.

Contributing

Contributions are very welcome. Please see Contributions for more details.

Data

Some toy datasets are available in Data.

Database

Schematics of the database structure used by VoDEx is available in Database.

GUI

For a quick start with napari-vodex see napari_vodex.

License

Distributed under the terms of the [BSD-3] license, vodex is free and open source software.

Citing VoDEx

If you use VoDEx in your research, please cite our paper:

Anna Nadtochiy, Peter Luu, Scott E Fraser, Thai V Truong, VoDEx: a Python library for time annotation and management of volumetric functional imaging data, Bioinformatics, Volume 39, Issue 9, September 2023, btad568, https://doi.org/10.1093/bioinformatics/btad568