Digital images are a ubiquitous way to represent phenotypes. More and more ecologists and evolutionary biologists are using images to capture and analyze high dimensional phenotypic data to understand complex developmental and evolutionary processes. As a consequence, images are being collected at ever increasing rates, already outpacing our abilities for processing and analysis of the contained phenotypic information.phenopype is a high throughput phenotyping package for the programming language Python to support ecologists and evolutionary biologists in extracting high dimensional phenotypic data from digital images. phenopype integrates existing state-of-the-art computer vision functions (using the OpenCV library as a backend), GUI-based interactions, and a project management ecosystem to facilitate rapid data collection and reproducibility.phenopype offers three different workflow types that support users during different stages of scientific image analysis (prototyping, low-throughput, and high-throughput). In the high-throughput workflow, users interact with human-readable YAML configuration files to effectively modify settings for different images. These settings are stored along with processed images and results, so that the acquired phenotypic information becomes highly reproducible.phenopype combines the advantages of the Python environment, with its state-of-the-art computer vision, array manipulation and data handling libraries, and basic GUI capabilities, which allow users to step into the automatic workflow when necessary. Overall, phenopype is aiming to augment, rather than replace the utility of existing Python CV libraries, allowing biologists to focus on rapid and reproducible data collection.