Project 7

3D+time image segmentation methods

Supervisor: Prof. Dr. K. Mikula, co-supervisors: local: Prof. Dr. Mariana Remesikova, external: Dr. J. Gehrig (P9)


Novel segmentation methods for 4D images of embryo development, as basis for cell tracking and lineage tree reconstruction algorithms: mathematical modelling in image processing & analysis, design of numerical methods for solving PDEs, efficient (parallel) computer implementation of numerical algorithms, high-performance computing (HPC) strategies.

Expected Results:

  • Research: New mathematical models and numerical methods for 3D+time image segmentation, tested & tuned on real microscopic data, implemented on modern parallel computer architectures and used as transferable skills.
  • Specific Outreach: An interactive image processing software presentations to use in school presentations
  • Specific Employability: Companies dealing with algorithm & software design, image analysis or engineering simulations


  • Academic: P3 CNRS, N. Peyriéras, Data format and specificities of zebrafish image data with respect to segmentation P4 UCAM, M. Zernicka-Goetz, Specific requirements for segmentation with mouse image data.
  • Industrial: P10, Tatramed Softw, Jozef Urbán, efficient implementation in medical image analysis software.

Links to other projects: ESR4,6& 10: image specificities according to biological material; ESR9,12&14: formats to fuel the segmentation software; ESR11: output formats for modelling; ESR13: implement in industrial & commercial applications.