Developing Super-resolution cryo-fluorescence microscopy and its correlative combination with Cryo-focused ion beam scanning electron microscopy and soft x-ray microscopy as an innovative tool in biomedical research and diagnostics

Supervisor Organisation PhD Awarding Entity: phd location
Aalen University
Aalen University
Aalen University, Germany

Research Focus

The project is designed such that the technological development drives the biomedical research question and vice versa. In close collaboration with the partners and based on their established workflows, we will correlate 3D microscopy techniques under cryogenic conditions (super-resolution FM, FIBSEM and SXT) and work towards an unprecedented hybrid imaging platform.

This will increase throughput and help us tackle a variety of exciting and outstanding biomedical research questions, including autophagy, nanoparticle-based chemotherapies, or microsporide infection. For example, the novel approach will allow us to visualize autophagy upon oxidative stress both at the molecular (super-resolution fluorescence microscopy) and ultrastructural level (FIBSEM and SXT).

Autophagy is a mechanism utilised by cells for major rearrangements and recycling of their content for bulk removal of damaged or unwanted organelles or damaged macromolecules, and is also important in metabolic stress situations. Tackling this intricate research question mechanistically will critically depend on the correlation of the mentioned imaging techniques to assess autophagosomes and their cargo under Abbe’s diffraction limit within their sub-cellular context in a close-to-native state.

Our vision is to expedite a mechanistic multiscale understanding of biology and bring CLEM to the next level by integrating cryo-FIBSEM and cryo-SR FM into one readily accessible hybrid instrument to facilitate sample handling and improve throughput – analogously to hybrid clinical imaging setups, such as Positron Emission Tomography together with Computed Tomography. Such hybrid setups do not require the relocation of the sample from one imaging platform to another, which comes with many challenges that limit throughput, including re-identification of the ROI or contamination during the transfer (specifically under cryo-conditions). Our long-term vision focuses on building CMI workflows even beyond volume CLEM and allow to zoom in from endogenous tissue or even living organisms to individual subcellular structures and relate their molecular dynamics to their overall anatomy.


As a SR technique, we choose structured illumination microscopy (cryo-SIM) that achieves a twofold increase in lateral resolution compared to conventional FM through structured illumination of the sample and generation of Moiré fringes, and, in addition, allows for optical sectioning of the sample.

For 3D-SIM, we will need to set up both hardware and robust image reconstruction algorithms. As 3D electron microscopy technique, we choose Focused Ion Beam Scanning Electron Microscopy. Further methods will focus on micropatterning and automated data processing and handling.

This project will lay the basis for us to work towards increasing throughput and implementing the system as a hybrid integrative setup of combined cryo-FIBSEM and cryo-SR FM, in close collaboration with industrial partners.

Aim 1

Building Correlative Cryogenic Super-Resolution Fluorescence Microscopy and Focused Ion Beam Scanning Electron Microscopy (Advanced Cryogenic 3D CLEM under the diffraction limit)

Aim 2

Automating the 3D CLEM Workflow by (i) establishing a hybrid imaging platform, (ii) micropatterning EM sample carriers, and (iii) setting up automated data processing (segmentation and correlation)

Aim 3

Showcasing the functionality and immense potential of our novel workflow based on long-standing biomedical questions

Pictures Attached

Image description: An advanced 3D CLEM workflow will be established under cryogenic conditions below the diffraction limit to highlight the mechanisms of nanoparticle-based chemotherapy, for example.



Role/Focus of PhD:

  • The PhD candidate will work on driving and automating method development (both hard- and software) to tackle biomedical research. This role will give opportunity to use Correlative Cryogenic Super-Resolution 3D CLEM.
  • The PhD candidate can apply the newly developed workflow to tackle exciting biomedical
    research questions (such as, nanoparticle-based chemotherapy) in proof-of-principle
  • Experience in both light and electron microscopy
  • Experience in image analysis (Matlab)


Application Deadline: 18th August 2023 (Closed)