Introduction

Bio-Volumentations is an image augmentation and preprocessing package for 3D (volumetric), 4D (time-lapse volumetric or multi-channel volumetric), and 5D (time-lapse multi-channel volumetric) biomedical images and their annotations.

The library offers a wide range of efficiently implemented image transformations. This includes both preprocessing transformations (such as intensity normalisation, padding, and type casting) and augmentation transformations (such as affine transform, noise addition and removal, and contrast manipulation).

The Bio-Volumentations library is a suitable tool for image data manipulation in machine learning applications. It can be used with any major Python deep learning library, including PyTorch, PyTorch Lightning, TensorFlow, and Keras.

This library builds upon wide-spread libraries such as Albumentations and TorchIO (see the Contributions section below). Therefore, it can easily be adopted by developers.

The source codes and more details are also available at the project’s GitLab page and at the project’s PyPi page.