James Swoger

EMBL Barcelona, Spain

McMaster University, Dept. of Engineering Physics Hamilton, Ontario, Canada Doctor of Philosophy 1992 – 1997 Dissertation: “On Non-uniform Pumping Effects in Semiconductor Lasers”, Supervisors: Drs. J.G. Simmons & D.A. Thompson. Master of Engineering 1989 – 1992 Dissertation: “Theory of the Multi-terminal Double-Heterostructure Opto-Electronic Switch” , Supervisor: Dr. J.G. Simmons. Bachelor of Engineering, ranked 4th/25 1985 – 1989 Mesoscopic Imaging Facility, EMBL Barcelona Barcelona, Spain Head of Facility 2017 – present • Supervising the Mesoscopic Imaging Facility • Developing optical imaging technologies for meso-scale biological samples Systems Biology Program, Centre for Genomic Regulation Barcelona, Spain Staff Scientist 2006 – 2017 • Supervision of imaging & microscopy projects • Design and implementation of a hybrid OPT/SPIM imaging platform • Development of software for control of microscope hardware Human Genetics Unit, Medical Research Council Edinburgh, U.K. Postdoctoral Researcher 2005 – 2006 • Implementation & testing of a laser-scanning Optical Projection Tomography system • Development of software for reconstruction of OPT images • Development of software for analysis of cell cycle time data European Molecular Biology Laboratory Heidelberg, Germany Officer Responsible for Advanced Microscopy 2003 – 2005 • Algorithm & software development for processing of multi-view microscopy data • Development of Selective Plane Illumination Microscopy (SPIM) European Molecular Biology Laboratory Heidelberg, Germany Senior Project Assistant 1999 – 2003 • Optical design and implementation of the Multiple Imaging Axis Microscope (MIAM) • Analysis of Optical Scanning Holography (OSH) for biological applications European Molecular Biology Laboratory Heidelberg, Germany Postdoctoral Researcher 1997 – 1999 • Design and realization of a Fiber-Coupled Single-Lens Confocal Theta Microscope • Modeling of optical phenomena in confocal microscopy McMaster University, Dept. of Engineering Physics Hamilton, Ontario, Canada Graduate Student 1990 – 1997 • Extensive characterization and modeling of semiconductor lasers • Opto-electronic switch modeling, design, and characterization

Cell 3D Positioning by Optical encoding (C3PO) and its application to spatial transcriptomics

Authors: James Cotterell, Jim Swoger, Spiros Bakas, Fumio Nakaki, Alexandre Robert-Moreno, Heura Cardona, Marco Musy & James Sharpe Most current state-of-the-art spatial -omics techniques require physically cutting the biological tissue of interest into thin slices, and are therefore intrinsically 2D methods. However, for many modern biological questions the 3D context is key. I will present our work on Cell 3D Positioning by Optical encoding (C3PO), in which we use a light-sheet microscope to optically write a pattern of 3D fluorescent gradients into an intact sample. Once this is done, the sample can be dissociated into individual cells on which transcriptomics, for example, can be performed. By dissociating the cells we lose the information about their original spatial positioning. However, because we have written the 3D fluorescence gradients into the cells before dissociation, after dissociation these fluorescent levels can be read by a FACS machine and used to map each individual cell back into the 3D space of the sample. Transcriptomics can then be done on cells whose original 3D positions in the sample are known.