acia-workflows: Automated Single-cell Imaging Analysis for Scalable and Deep Learning-based Live-cell Imaging Analysis Workflows

Live-cell imaging (LCI) technology enables the detailed spatio-temporal characterization of living cells at the single-cell level, which is critical for advancing research in the life sciences, from biomedical applications to bioprocessing. High-throughput setups with tens to hundreds of parallel cell cultivations offer the potential for robust and reproducible insights. However, these insights are obscured by the large amount of LCI data recorded per experiment. Recent advances in state-of-the-art deep learning methods for cell segmentation and tracking now enable the automated analysis of such large data volumes, offering unprecedented opportunities to systematically study single-cell dynamics. The next key challenge lies in integrating these powerful tools into accessible, flexible, and user-friendly workflows that support routine application in biological research. In this work, we present acia-workflows, a platform that combines three key components: (1) the Automated live-Cell Imaging Analysis (acia) Python library, which supports the modular design of image analysis pipelines offering eight deep learning segmentation and tracking approaches; (2) workflows that assemble the image analysis pipeline, its software dependencies, documentation, and visualizations into a single Jupyter Notebook, leading to accessible, reproducible and scalable analysis workflows; and (3) a collection of application workflows showcasing the analysis and customization capabilities in real-world applications. Specifically, we present three workflows to investigate various types of microfluidic LCI experiments ranging from growth rate comparisons to precise, minute-resolution quantitative analyses of individual dynamic cells responses to changing oxygen conditions. Our collection of more than ten application workflows is open source and publicly available at https://github.com/JuBiotech/acia-workflows.