Interdisciplinary work is an increasingly frequent and important aspect of scientific research. However, successful knowledge exchange and collaboration between experts is itself a challenging activity with both technical and social components that require consideration. Here, this article analyses the cultural factors involved in interdisciplinary research, specifically in the context of a software programme designed to improve knowledge exchange. The authors undertook an ethnographic study to understand the impact of virtualisation and visualisation on an interdisciplinary research team, working together to develop novel imaging technologies for investigating stem cells. In this discovery-research environment the challenge was to determine the socio-technical effect of an in-house software tool called ProtocolNavigator, which provided a virtual laboratory environment for the team to simulate and map their ‘real-life laboratory’ activities. This display, together with activity icons and a timeline, could be visually analysed and transferred between multi-institutional researchers in a non-narrative approach. The aim of the work reported here is to provide the first detailed analysis of how software of this type is used in practice, and to analyse this through a robust social science-based perspective. Subsequently this study examines the effectiveness of this virtual laboratory environment on enhancing communication and understanding using a theoretical framework drawing upon three insights from the Sociology of Expertise and Experience: (i) interactional and contributory expertise, (ii) knowledge exchange and interpretative flexibility, and (iii) trading zones. The framework was extended by introducing the notion of material, concept and practice trade at these trading zones with a demonstration of how interactive visualisation of interconnected trading routes can empower interdisciplinary work. The addition of Foucault’s classic account of power found evidence of a panoptical effect due to the augmented visibility of each other’s work. In summary, the article offers a theoretical framework together with novel analysis to determine the influence of introducing tools and approaches designed to enhance interdisciplinary working—particularly in the context of knowledge sharing and trust.