Project A-Heilemann, Area A: Microscope technology and image acquisition

PhD Position: Super-Resolution Microscopy and Quantitative Image Analysis for Optical Cell Biology

Scientific background

Super-resolution fluorescence microscopy makes it possible to visualise the nanoscale organisation of proteins directly in their cellular context. Single-molecule localisation microscopy methods such as DNA-PAINT go one step further: beyond images with near-molecular resolution, they provide quantitative information, for example on protein copy numbers, oligomeric states and the spatial arrangement of multi-protein complexes.

Using this potential for optical cell biology requires progress on two fronts at once: experimental methods that label and image target molecules efficiently, in multiple colours and with minimal perturbation, and computational methods that turn large single-molecule datasets into robust, quantitative biological results. The Single-Molecule Biophysics group works on both, including weak-affinity labelling for long-term single-molecule imaging in living cells and deep neural networks that accelerate DNA-PAINT acquisition and simplify data reconstruction.

Your project

The aim of this doctoral project is the methodological and experimental development of super-resolution microscopy for optical cell biology, together with new approaches for computational quantitative image analysis. The work includes:

1. developing and optimising super-resolution and single-molecule imaging methods for cellular structures
2. establishing labelling and imaging strategies for multi-target and live-cell single-molecule experiments
3. developing computational tools, including machine-learning approaches, for the quantitative analysis of super-resolution data
4. validating the methods in cell biological model systems and extracting quantitative information on protein organisation
5. collaborating with experimental and computational partner projects within iMOL

Your profile

Required

• Completed university degree (Master’s or equivalent) in chemistry, biophysics, physics, biochemistry or a related discipline
• Strong interest in super-resolution microscopy
• Very good written and spoken English
• Motivation for interdisciplinary work between experiment and computation

Advantageous

• Experience in super-resolution microscopy
• Experience in fluorescence microscopy of cell biological structures
• Experience in computational image analysis
• Programming skills, for example in Python

What we offer

An excellent environment for competitive research, several state-of-the-art super-resolution microscopy systems and integration into research networks across Goethe University. The position is embedded in the DFG Research Training Group iMOL (GRK 2566), which provides a structured doctoral programme with lectures, workshops, retreats and an annual Winter School, as well as access to the Frankfurt Center for Advanced Light Microscopy (FCAM).

How to apply

Please send your application as a single PDF (cover letter stating that you apply for project A-Heilemann, CV, transcripts, names of two referees) by 15 November 2026 to imol.coordinator@biophysik.org or directly to the office of Prof. Heilemann at S.Wegner@em.uni-frankfurt.de. Costs arising from the application process cannot be reimbursed.

Key publications

Familiarity with the scientific context of the group’s recent work is appreciated in the application.

1. Saguy A, Xiao D, Narayanasamy KK, Nakatani Y, Saliba N, Gagliano G, Gustavsson A-K, Heilemann M, Shechtman Y. One-click reconstruction in single-molecule localization microscopy via experimental parameter-aware deep learning. npj Imaging 2025, 3:61. doi:10.1038/s44303-025-00123-w
2. Catapano C, et al. Long-term single-molecule tracking in living cells using weak-affinity protein labeling. Angewandte Chemie International Edition 2025, 64:e202413117. doi:10.1002/anie.202413117
3. Narayanasamy KK, Rahm JV, Tourani S, Heilemann M. Fast DNA-PAINT imaging using a deep neural network. Nature Communications 2022, 13:5047. doi:10.1038/s41467-022-32626-0

Goethe University is committed to equal opportunity, family friendliness and diversity. Applications from people with a migration background and from other underrepresented groups are particularly welcome. Applicants with a severe disability or equivalent status will be given preference in cases of equal suitability. Where women are underrepresented in the department, they will be given preference in cases of equal qualification.

Data protection: personal data contained in your application are processed solely for the purpose of the selection procedure (Art. 88 GDPR in conjunction with § 23 HDSIG) and are not kept longer than required for the procedure and any related legal claims. Details are provided in the privacy policy of Goethe University Frankfurt.