For more than three centuries we have been watching and studying microscopic phenomena behind a microscope. We discovered that cells live in a physical environment whose predominant factors are no longer those of our scale and for which we lack a direct experience and consequently a deep intuition. Today’s computational approaches to microscopy allow high frame rate volumetric reconstructions from 2D holographic patterns that encode the full 3D structure of the sample. On a parallel track, modern holographic spatial light modulators integrated in optical tweezers setups allow to dynamically arrange complex many-particles systems in precise 3D configurations. In this regard, highly efficient iterative algorithms ensure quick hologram computation for the live refresh of the spatial light modulator. In this PhD thesis, we present a novel instrument which, by integrating holographic and virtual reality technologies, allows the user to be completely immersed in a dynamic virtual world which is the simultaneous replica of a real system under the microscope. We use a 3-axis implementation of holographic microscopy for fast 3D imaging and real-time rendering on a virtual reality headset. At the same time, hand tracking data is used to dynamically generate holographic optical traps that can be used as virtual projections of the user hands to interactively grab and manipulate ensembles of micro-particles or living motile cells, like swimming bacteria. The strategy used can be flexibly adapted to different sample types by integrating suitable 3D imaging techniques into the system. The dynamics of larger eukaryotic cells is observed using the gradient light interference microscopy label-free technique, which provides quantitative height maps of the specimen. Our interface allows a more direct interaction with systems at the micron scale. The user can immersively explore a microscope sample of colloidal particles or living cells, analyze their motility interactively and with quantitative tools, control optical traps to ...