Imaging Physics in Medicine

• Mark Ladd (Medical Physics in Radiology, German Cancer Research Center (DKFZ))

Macroscopic imaging in medicine is used both for clinical diagnostics and therapy planning in human patients as well as in research, where both human and small-animal imaging play an important role. Medical imaging is based on several physical principles ranging from ultrasound to ionizing radiation coming from sources outside or inside the patient. Accordingly, the questions to be answered by the different methods and the information in the resulting images are quite different. In this lecture, the physical and technical principles of techniques such as computer tomography (CT), positron emission tomography (PET), and magnetic resonance imaging (MRI) will be introduced.

Analyzing Medical Images Using Machine Learning

• Paul Jäger (Helmholtz Imaging, DKFZ)
• Lukas Klein (Helmholtz Imaging, DKFZ)

The success of Machine Learning has revolutionized the field of medical image analysis in the past 5 years. This talk will give an introduction to relevant concepts in machine learning with a focus on computer vision. Subsequently, several example applications in the biomedical domain will be discussed to study the current state of research and the associated challenges and opportunities.

Optical Coherence Tomography in Biofilm Research - Visualization and Characterization of the Mesoscopic Biofilm Structure

• Michael Wagner (KIT)

Understanding the biofilm structure is important in order to understand the structure-function relations of biofilm systems. For decades microscopic tools have widely been applied visualizing the microscopic structure of biofilms (e.g., distribution of cells within the matrix of extracellular polymeric substance). However, mass transport and transfer occurs at a larger scale (mesoscale, mm-scale). By applying optical coherence tomography (OCT) the mesoscopic biofilm structure is assessed non-invasively, in situ and with almost no sample preparation. OCT thus has become popular in biofilm research within the last 10 years. This lecture will introduce OCT and provide insights into the technology and possible outputs (e.g., structure analysis).

Basics of Light Microscopy for the Study of Cells

• Rudolf Merkel (FZJ)

Light microscopy is one of the most important techniques for the investigation of animal cells. In this lecture I will present basics of widely used light microscopy techniques including fluorescence and confocal fluorescence microscopy as well as their application on living cells.

Advanced Fluorescence Microscopy

• Gerd Ulrich Nienhaus (Institute of Applied Physics, KIT)

After a brief, general introduction into fluorescence microscopy, I will focus on three modern modalities, STimulated Emission Depletion (STED) nanoscopy, Single-Molecule Localization Microscopy (SMLM) and Light Sheet Microscopy (LSM). STED and SMLM are powerful techniques for cellular imaging with nanoscale spatial resolution, whereas LSM is an excellent and versatile imaging method with diffraction-limited resolution and low phototoxicity. Pros and cons of the methods for particular imaging applications will be discussed.

Microscopy Assessment of DNA-based Information Processing in Biological and Artificial Systems

• Lennart Hilbert (KIT)

The processing of DNA sequence information is a central task of biological cells, and could in the future enable molecular biotechnologies with “smart capabilities”. In our research group, we combine cutting-edge light microscopy, computational data analysis, and simulations to understand the principles of this information processing in the 3D-space of the cell nucleus. In this lecture, I will outline how such imaging-informed assessments can reveal major principles of DNA-based information processing, and how these principles might in the future guide the design of artificial, DNA-based information systems.

Imaging Biological Molecules by Electron Cryo-Microscopy (cryo-EM)

• Carsten Sachse (Forschungszentrum Jülich GmbH, Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons / ER-C-3 Structural Biology, Institute for Biological Information Processing / IBI-6 Cellular Structural Biology)

The cryo-EM method has become very powerful in the past several years and it is becoming the method of choice for many structural biologists. The interpretation of single noisy molecular images in solution still presents an obstacle for obtaining faithful structural information of biological macromolecules. Therefore, we routinely apply image processing routines of structural averaging in single-particle cryo-EM as well as cryo-tomography. Small quantities of purified proteins and protein complexes can be visualized in vitreous ice using single-particle cryo-EM. Subsequent data processing of 1000s of molecular images enables three-dimensional structure determination at near-atomic resolution. The obtained atomic models provide the chemical framework for biological macromolecules with respect to their biological function. Alternatively, more complex biological environments such as cells are increasingly being visualized by cryo-EM methods. Electron cryo-tomography combined with fluorescence light microscopy enables the detailed characterization of natively preserved cells, the organelle ultrastructures and provides the link to their molecular interpretation. In the talk, we will explain the physical foundations of the cryo-EM techniques and associated image processing approaches and combine them with recently developed applications that assist in the interpretation of the native electron cryo-micrographs.