deepthought: domain driven design for microscopy with applications in DNA damage responses

Microscope systems have traditionally separated data acquisition and analysis into distinct phases, limiting real-time insights and experimental adaptability. While open-source tools exist for device control, there remains a need for integrated software frameworks that combine acquisition and analysis. Here we present deepthought, a framework built on domain-driven design principles that unifies microscope control and data analysis through a common domain language. This framework enables automated high-throughput imaging with real-time analysis capabilities, demonstrated through studies of DNA damage responses in live cells. By implementing deepthought on a standard wide-field microscope, we achieved sample sizes exceeding 10,000 cells per condition and identified rare cellular subpopulations, capabilities typically limited to specialized high-content systems. Our approach provides a foundation for developing context-aware microscopy software that can dynamically adjust experimental parameters based on real-time analysis of biological phenomena.