Pre-announcement · PhD position · CTU in Prague · FNSPEOfficial call to follow

MIND-MAP · a funded PhD on microglia

From branches to brain states.

What does it mean when a brain cell changes its shape? Build the geometry and topology that turn 3D + time microscopy into a quantitative language for brain states.

Illustration: computer-generated cells,
not microscopy data
Start
1 Mar 2027
Positions
PhDfunded opening
Funding
3 years2027–2029
Where
PragueCTU · FNSPE

What you'll work on

Hybrid Partial Differential Equations (PDEs) + deep-learning segmentation PDE · DL

3D segmentation that keeps thin branches.

Scale-aware volumetric representations multi-scale

Cell shapes that hold across scales.

Tracking in 3D + time live imaging

How shapes change over time.

Geometry-informed TDA geometry · topology

What shape changes mean.

The project combines mathematical method development with real, challenging biological data — the goal is not merely to apply existing PDE/ML tools, but to develop new combinations.

CTU PI: Jooyoung Hahn (CTU Prague; computational modelling). MIND-MAP partners: Paweł Dłotko (University of Warsaw; Topological Data Analysis) and Sandra Siegert (ISTA, Austria; microglia biology and imaging).

What you get

  • Funded PhD position (≈ 43,000 CZK net a month) within the international MIND-MAP project
  • A research problem at the intersection of geometry-informed Topological Data Analysis, PDEs and deep learning in real scientific data
  • Close collaboration with researchers in Warsaw and at ISTA
  • Access to unique 3D and 3D+time microscopy datasets
  • Opportunities for conferences and research visits

Who we are looking for

  • PhD candidates: a master's degree in mathematics, applied mathematics, computer science, physics or a related quantitative field
  • Strong background in numerical analysis and interest in topology, geometry or data analysis
  • Readiness to program — Python and/or C++
  • Good English, and curiosity, dedication, willingness, good teamwork and positivity about interdisciplinary research

How it works

  1. NowBy 20 Nov 2026 — send a CV, add a few lines about your research interests and what you can bring.
  2. NextInformal contact — we can discuss the project and how the project fits your background, for selected candidates.
  3. Official callFormal recruitment and eligibility criteria will be announced separately. Approximate application deadline: mid-December 2026.
  4. 2027The position begins on 1 Mar 2027.

This page is a pre-announcement and does not constitute the formal recruitment notice.

Interested in the PhD position? Get in touch.

If a combination of geometry-informed Topological Data Analysis, PDEs and deep learning in real scientific data sounds interesting, feel free to contact me already now. Send a CV, add a few lines about your research interests and what you can bring. This is a pre-announcement; the official recruitment calls, including formal conditions, will be published separately.

jooyoung.hahn@fjfi.cvut.cz