The MIND-MAP project (2027-2029), a collaboration of CTU in Prague, the University of Warsaw and ISTA Austria, is hiring one PhD student and one postdoc in Prague and one PhD student and one postdoc in Warsaw (Pre-announcement).

MIND-MAP studies how microglia, the immune cells of the brain, change their branching shape in 3D + time microscopy, and turns these images into a quantitative, geometric and topological readout of brain state. Both groups work closely with Sandra Siegert's lab at ISTA, with access to unique 3D and 3D + time microscopy data. The goal is to develop new mathematics, not merely to apply existing tools.

In Prague (CTU in Prague, FNSPE, with Jooyoung Hahn), the work covers dimensionality reduction, hybrid PDE + deep-learning segmentation, scale-aware 3D shape representations, tracking in 3D + time, and geometry-informed TDA.

In Warsaw (University of Warsaw, with Pawel Dlotko), it covers topological descriptors of shapes that change in time, shape trajectories, Ball Mapper and interpretable visualization.

We are looking for candidates with a strong background in (applied) mathematics, computer science, physics or a related field, and a strong interest in biology. Postdoc candidates should have experience in one of the following areas: numerical PDEs, image segmentation, deep learning, TDA or geometry

Prague salary: postdoc 70,000 CZK gross per month, full time, start 1 January 2027 (negotiable); PhD 38,745 CZK gross per month (0.8 FTE) plus a 12,000 CZK tax-free stipend (about 43,000 CZK net), start 1 March 2027.

To apply, send a CV and a few lines about your research interests and what you can bring, and say whether you apply for the PhD or the postdoc: