PhD Position (m/f/d)

"AI-assisted reconstruction of Fourier light field micro- and mesoscopy data for the quantitative investigation of brain functions’ biomedical processes"

Institution: Institute of Cellular Neurophysiology, Hannover Medical School (MHH), Germany
Start date: As soon as possible (negotiable)
Contract: 3 years (fixed term), remuneration according to TV-L E13 (German public sector salary scale
Working language: English (German not required)

Project in brief: Understanding how the brain processes information—especially during learning—requires fast, quantitative functional imaging across scales. Conventional serial-scanning microscopy cannot capture rapid, volumetric dynamics at low photon counts. This PhD project aims to develop a photon-aware AI-driven framework for real-time 3D reconstruction and quantitative analysis of weak fluorescence signals (e.g., from Ca2+ indicators) from Fourier Light-Field Micro- and Mesoscopy (FLMM) raw data.

Your tasks

  • Design and implement DL-based algorithms for 3D image reconstruction and denoising tailored to photon-limited microscopy data.
  • Build GPU-accelerated, low-latency pipelines that enable real-time detection of biological events (e.g., calcium transients).
  • Work closely with optical engineers and neuroscientists within the consortium
  • Validate and compare your approach on primary brain slices and organotypic 3D brain cultures.
  • Contribute to open-source code, documentation, and reproducible analysis workflows.
  • Present results at conferences and in scientific publications.

Your profile

  • Master’s degree (or equivalent) in computer science, electrical/biomedical engineering, physics, applied mathematics, computational neuroscience, or a related field.
  • Solid programming skills in Python; high familiarity with deep learning frameworks (e.g., PyTorch or TensorFlow).
  • Experience or strong interest in one or more of the following: image processing, machine learning, computational imaging/optics, inverse problems, or statistical modelling of noisy data.
  • Curiosity for neuroscience applications and enjoyment of interdisciplinary teamwork.
  • Good English communication skills. German is not required and can be learned on the job.

What we offer

  • A scientifically ambitious project with clear application to dynamic brain processes.
  • Access to state-of-the-art microscopy, advanced image analysis infrastructure, and the MHH high-performance computing cluster.
  • Close collaboration with LUH optical engineering and MHH biomedical labs; opportunities to co-design algorithms with hardware and biology.
  • Supervision by an experienced, supportive team; professional development and conference participation.
  • The group language is English, so no German language skills are required – but it is a great opportunity for you to learn German!
  • Salary and conditions according to TV-L E13; family-friendly and inclusive workplace. Applications from women are especially encouraged. Applicants with disabilities will be given preference in case of equal qualification.

How to apply

Please submit your application to zeug.andre@mh-hannover.de

Include:

  • Cover letter (motivation and relevant experience)
  • CV (including links to code repositories, if available)
  • Degree certificates and transcripts (Bachelor’s and Master’s)
  • Contact details of one referee
  • Prefered starting date

Application review begins immediately and continues until the position is filled.

 

Data protection

Applications will be processed solely for recruitment purposes in accordance with applicable data protection regulations (e.g., GDPR).