Advances in 3D Imaging and Analysis

Thursday, 20 April • 1:30 p.m. – 3:30 p.m.

This session will explore the development and application of the latest innovations in imaging hardware and software for extracting knowledge from 3D model systems. We will discuss best practice tools and techniques for imaging in 3D including:

• Sample preparation
• Optimization of 3D screening assays
• Image analysis
• Downstream data handling

We will present case studies demonstrating tangible examples of when 3D imaging is required and provides an added benefit over traditional 2D assays. Finally, we will discuss unresolved challenges of 3D imaging and analysis and where concerted multidisciplinary research effort is required to advance the field.

Session Chair:

Marc Bickle, Ph.D. (Roche)
Bickle obtained his Ph.D. at the Biozentrum in Basel, Switzerland, studying the immunosuppressive drug Rapamycin. He then went to the Laboratory of Molecular Biology in Cambridge, UK, to study the genetics of behavior in C. elegans. Afterward, he participated in the creation of Aptanomics, a drug discovery Biotech in Lyon, France, developing yeast 2 hybrid screens to select a collection of peptide aptamers. After this period in biotechnology, he headed the High-Content Screening facility at the Max Planck Institute of Molecular Cell Biology and Genetic (MPI-CBG) in Dresden, Germany, performing functional genomic and chemical screens using automated microscopy. Since 2021, Marc has been leading the Organoid Phenotyping platform at the Institute for Human Biology at pRed, Roche in Basel, Switzerland.

Speakers:

Peter Horvath, Ph.D. (Institute of Biochemistry, Biological Research Centre, Szeged, Hungary)
Life Beyond the Pixels: Single-Cell Analysis Using Deep Learning and Image Analysis Methods
Horvath is currently the director and a group leader at the Biological Research Center in Szeged, Hungary, and holds a Finnland Distinguished Professor Fellow position at the Institute for Molecular Medicine Finland, Helsinki. He graduated as a software engineer and received his Ph.D. from INRIA and the University of Nice, Sophia Antipolis, France in satellite image analysis. Between 2007 and 2013, he was a senior scientist at ETH Zurich in the Light Microscopy Centre. He is interested in solving computational cell biology problems related to light microscopy and is involved in four main research fields; 2/3D biological image segmentation and tracking; development of microscopic image correction techniques; machine learning methods applied in high-throughput microscopy and the development of single-cell isolation methods. He is the co-founder of the European Cell-based Assays Interest Group and the councilor of the Society of Biomolecular Imaging and Informatics.

Hugh Sparks, Ph.D. (Imperial College London)
High-Speed and High-Content Light-Sheet Fluorescence Microscopy
Sparks received a masters degree in physics from The University of Manchester and a Ph.D. in physics from Imperial College London. During his Ph.D., they developed novel time-resolved fluorescence imaging endoscope technologies for biomedical applications. They later worked in Erik Sahai’s Tumor Cell Biology Lab at The Francis Crick Institute to investigate the application of time-resolved fluorescence imaging endoscopy to pre-clinical imaging of drug-target engagement during chemotherapy. Currently, they are working as a Cancer Research UK (CRUK) funded postdoctoral researcher in Chris Dunsby’s and Paul French’s photonics labs at Imperial College London and as a visiting researcher at The Institute of Cancer Research (IRC) and The Francis Crick Institute. The primary scope of the work is to develop new tools to enable higher throughput and time-lapse 3D imaging of samples arrayed in multi-well plates for cancer research.

Jan Bruder, Ph.D. (Roche)
Automated Cell Type-Specific High Throughput Screening Technology for Human Midbrain Organoids 

Philipp Wahle, Ph.D. (ETH Zurich)
Multi-Modal Spatiotemporal Phenotyping of Human Retinal Organoid Development