Software

BioEncoder: a metric learning toolkit for comparative organismal biology

BioEncoder is a Python package for metric deep learning, crafted for ease of use and flexibility across diverse datasets. It features taxon-agnostic data loaders, custom augmentation options, and streamlined hyperparameter adjustments through text-based configuration files. The toolkit’s significance lies in its potential to unlock new possibilities in biological image analysis - from phenomics and disease diagnosis to species identification and ecosystem monitoring.

Visit https://github.com/agporto/BioEncoder to get started

phenopype: a phenotyping pipline for Python

phenopype is a high throughput phenotyping package for the programming language Python. It aims at supporting biologists in their efforts to extract high dimensional phenotypic data from digital images. phenopype provides high level functions for image processing that can be stacked and executed sequentially to efficiently process single images or large data sets. Users can interactively assemble their own function-stacks that can be customized and stored along with raw data for full reproducibility. Phenopype is designed to provide robust image analysis workflows that can be implemented with little or no Python experience.

Visit www.phenopype.org to get started, and check the gallery at www.phenopype.org/gallery/ for examples: