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 describe the phenotypic landscape of organoid maturation in a quantitative, 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. Currently, we further upscale our workflows by robotics and optimizing culturing conditions.
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. To increase the information content per organoid and cell, leading to a clearer picture of the underlying process, we develop novel multiplexing approaches specifically for complex three-dimensional structures.
Light-Sheet microscopy
We work in close collaboration with Viventis Microscopy Sàrl to further develop new light-sheet based imaging technologies tailored for 3D cell culture systems since 2016. The collaborative efforts allow the imaging of 3D cell culture systems (intestinal/colon organoids, gastruloids, etc) to be imaged at low light dosage for many weeks with high spatiotemporal resolution. Furthermore, we also push the development of new analysis workflows which enable the segmentation and feature extraction of the data collected in a multiscale approach, aiming at linking tracking and segmentation of single cells within the whole tissue perspective. With this we aim at creating unique opportunities to study self-organizing properties of organoids at high spatiotemporal resolution and throughput, quantifying all cell division, differentiation events and transcription factor dynamics during organoid development and homeostasis.
