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Mixed reality learning environments, offer opportunities to engage students in novel and potentially transformative learning experiences, but developing effective methodologies for examining how the environment mediates learning is often challenging. This paper draws on quantitative methods to examine larger patterns of interactions and deeper qualitative multimodal interaction analyses for investigating the role of embodiment in the collaborative learning process within mixed reality learning environments. This set of analyses is applied to the evaluation of ten students interacting with tablet computers, and large displays of scientific content and aggregated representations of their collective work. We examine how these resources are used for collaborative knowledge construction, illustrating embodied interactions between artefacts and people in the learning environment.