Image-based High-content screening
To unravel molecular mechanisms orchestrating the organoid formation and self-organization we use a high-content image-based screening platform developed in the lab. Our screening approach has a single-cell resolution and generates a multivariate feature set profiling hundreds of thousands of individual organoids that describes quantitatively the phenotypic landscape of organoid development in a robust and unbiased way. We used multivariate analysis of phenotypic screening data to generate perturbation-specific phenotypic fingerprints giving a detailed characterization of every condition. Phenotypic fingerprints are then used to infer regulatory genetic interactions and hierarchical relationships between phenotypes, establishing a novel paradigm in genetic interaction screening applied to emergent systems.
Single cells in space and time
Single-cell approaches that considers the spatial and temporal localizations of a cell within a collectivity are important for understanding how tissue homeostasis is preserved and how development and regeneration are regulated. Indeed, key and central players in all these phenomena are single cells communicating with each other and with the environment. Cellular decision-making is a probabilistic event that depends on the context of each cell at a specific moment in time. In the lab, we develop single-cell imaging and genomics technologies with spatial and temporal resolution and we use the combination of these rich datasets to understand key biological processes during development and regeneration.
We recently developed a new inverted light-sheet microscope specifically tailored to image organoid development. This imaging setup allows us to characterize the morphological steps involved in organoid development and provides unique opportunities to study self-organizing properties of organoids at high spatiotemporal resolution and throughput. Together with computer vision and machine learning approaches, this is enabling a complete tracking of single cells, quantifying all cell division, differentiation events and transcription factor dynamics during organoid development and homeostasis.