Modern scientific instruments are becoming essential for discoveries because they provide unprecedented insight into physical or biological events – often in real time. However, these instruments may generate large amounts of data, and increasingly they require sophisticated e-infrastructure for analysis, storage and archive. The increasing complexity and scale of the data, processing steps and systems has made it difficult for domain scientists to perform their research, narrowing the user base to a select few. In this paper, we present a framework that democratises large-scale instrument-based science, increasing the number of researchers who can engage. We discuss a prototype at the University of Queensland. The system is illustrated through two case studies, one involving light microscopy imaging of the innate immune system, and the other electron microscopy imaging of the SARS-CoV-2 viral proteins.