BioImageLoader: Easy Handling of Bioimage Datasets for Machine Learning

Abstract

BioImageLoader (BIL) is a python library that handles bioimage datasets for machine learning applications, easing simple workflows and enabling complex ones. BIL attempts to wrap the numerous and varied bioimages datasets in unified interfaces, to easily concatenate, perform image augmentation, and batch-load them. By acting at a per experimental dataset level, it enables both a high level of customization and a comparison across experiments. Here we present the library and show some application it enables, including retraining published deep learning architectures and evaluating their versatility in a leave-one-dataset-out fashion.