Surprisingly many long-standing questions in (stem) cell research remain disputed. One major reason is the fact that we usually analyze only populations of cells – rather than individual cells – and at very few time points of an experiment – rather than continuously.

We therefore develop imaging approaches and software to image, segment, and track cells, and to quantify e.g. divisional history, position, interaction, and protein expression or activity of all individual cells over many days and generations.

Live-cell imaging is complemented by novel large-volume multi-color 3D imaging with up to single-molecule sensitivity. Dedicated software, machine learning and computational modeling enable data acquisition, curation, and analysis. Custom-made microfluidics, optogenetics and other hardware devices improve single-cell observation, dynamic manipulation, molecular analysis, and the high-dimensional snapshot ‘omics’ quantification of individual cells with known history, kinship and dynamics.

The resulting continuous single-cell data is used for analysing the dynamics, interplay, and functions of signalling pathway and transcription factor networks in controlling the fate decisions of self-renewing and differentiating hematopoietic, pluripotent, neural stem and intestinal stem and progenitor cells and normal and synthetic embryos.