Organizers and Advisory Committee

Abhishek Kumar, MBL
Gary Laevsky, Princeton University

Advisory Committee
Dr. Courtney Akitake, Zeiss
Dr. Scott Fraser, University of Southern California
Dr. Elizabeth Hillman, Columbia University
Ms. Dana Mock-Muñoz de Luna, MBL – Administrative Support
Dr. Nipam Patel, MBL
Dr. Hari Shroff, NIH
Dr. Simon Watkins, University of Pittsburgh

Invited Speakers

Doing science with light sheet microscopy - in the lab and in the classroom


I will discuss a few, primarily developmental biology, projects that have been powered in my group by the light sheet technology. I will also briefly speak about how the challenges of light sheet data fuelled and continue fuelling the development of the Fiji platform. Finally, I will advertise the approach we took to teaching light sheet microscopy principles to the next generation of scientists during EMBO practical courses.

Pavel Tomancak studied Molecular Biology and Genetics at the Masaryk University in Brno, Czech Republic. He then did his PhD at the European Molecular Biology Laboratory in the field of Drosophila developmental genetics. During his post-doctoral time at the University of California in Berkeley at the laboratory of Gerald M. Rubin, he established image-based genome-scale resources for patterns of gene expression in Drosophila embryos. Since 2005 he leads an independent research group at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) in Dresden where he became senior research group leader in 2013.

His laboratory continues to study patterns of gene expression during development by combining molecular, imaging and image analysis techniques. The group has lead a significant technological development aiming towards more complete quantitative description of gene expression patterns using light sheet microscopy. The emphasis on open access resulted in establishment of major resources such as OpenSPIM and Fiji. The Tomancak lab is expanding the systematic analysis of gene expression patterns to other Drosophila tissues and employing the comparative approach in other invertebrate species to study the evolution of early development.


Dr. Adikes recently joined the Biology Department at Siena College in Loudonville, NY in the fall of 2021 where she teaches undergraduate Cell and General Biology. She completed her postdoc in the Matus and Martin Labs at Stonybrook University where she investigated cell invasion and migration in salamanders, zebrafish and C.elegans. Her lab at Siena College is focused on understanding the cytoskeletal regulation of cell migration during development in C. elegans. She and her students will use a variety of approaches to investigate cell migration from the atomic to organismal level in the years to come. She is passionate about training the next generation of biologists and shares with them her joy of being able to visualize and quantify awesome cell biology!

Anatomy of a light-sheet microscope


This presentation will review the basic structure and organization of a light-sheet microscope. We will examine what makes this type of microscope similar or different than conventional fluorescence microscopes since they share many of the same components such as objective lenses, filters, lasers detectors and more. Additionally, there are many different types of light-sheet microscopes with these components that are configured in different orientations to match the imaging needs of the researcher. We will discuss the parts of a basic light-sheet microscope and how these combine to provide improved speed and better depth of imaging with less damage to the sample.

With over 10 years of experience working in an imaging core facility, I consider myself to be a research facilitator more than a core manager. In addition to instrument training, I provide researchers with advice regarding sample preparation for microscopy including paraffin sectioning, ultramicrotomy, histochemical and immunocytochemical staining techniques. While at the Campus Microscopy and Imaging Facility at the Ohio State University, I gained expertise in live cell imaging, confocal microscopy, two-photon and intra-vital imaging, transmission electron microscopy and scanning electron microscopy. At the University of Notre Dame, I began using light-sheet microscopy to assist researchers with imaging zebrafish and Drosophila embryos, and organoid cultures using the Bruker MuVi SPIM system. Throughout my career in the imaging core, I have developed collaborative relationships with researchers that have led to co-authorships on publications, book chapters and presentations at scientific meetings. I have enjoyed learning about very diverse subjects such as cancer biology, veterinary science, bacterial biofilms research, and three-dimensional culture systems (hydrogels, collagen gels, polymeric microfibers), and I consider these relationships to be one of the most rewarding aspects of my work.

Considerations for light-sheet image processing and analysis


In the hands of curious life scientists and biomedical researchers, light-sheet microscopes can easily produce data that challenge the limits of commonly available computational resources. In this presentation, we overview relevant computing concepts that will aid researchers in choosing workable computing hardware and software solutions from the vast landscape of available options. We will also discuss strategies for planning experiments and creating image processing pipelines with specific quantifiable biological questions in mind and provide guidance on how to document this process for sharing and scientific reproducibility. 

We have yet to understand how embryonic brain development gives rise to brain function and how deficits in this process lead to brain disorders. To help improve this understanding, Holly Gibbs is interested in developing accessible microscopy, labeling, visualization, and bioimage informatics tools for creating multi-scale models of the emergence of brain structure and function. She earned her Ph.D. in Biomedical Engineering from Texas A&M University (TAMU) in 2014 studying neurodevelopment in zebrafish using multi-photon microscopy with Alvin Yeh and Arne Levken. She joined the TAMU Microscopy and imaging Center in March 2019, directed by Kristen Maitland, where she is currently funded as an Imaging Scientist by the Chan Zuckerburg Initiative. This grant program aims to provide imaging cores with support for accelerating the adoption of novel imaging techniques and open-source processing software at their institutions.

Can it fit? Tips and tricks to bring your sample into the light…sheet

The light sheet illumination is a very specific of an orthogonal arrangement to the detection. This brings challenges and some drawbacks. The inherent possibility to rotate the sample and the ever-growing geometrical arrangement out there requires some basic guidelines to best prepare your samples. From disappearing light sheet to cleared samples and 140 acronyms we will walk towards the light and give you a few tricks on how to get your sample right and even to design and create your own open-source sample holder to share with the community.

Biologist by training, tinkerer by birth and French by default, Emmanuel Reynaud has been involved in light sheet microscopy for more than a decade but also run an imaging platform on a schooner TARA OCEANS (2009-2012) that circumvent the world looking at ocean health. Alongside Pavel Tomancak they ran the light sheet community organizing yearly conferences and international microscopy courses putting the technology on the map and helping companies tagging along. His group works with companies as well as NGOs and academic groups, it holds several patents and take part in 2 companies. The group currently works on bringing light sheet into the wild, underwater and below ice caps.

3d Microscopy For Quantitative Analysis Of Microcarrier-Based Stem Cell Cultures


Mesenchymal stem cells (MSCs) show great potential as therapies for various diseases. Three-dimensional microcarrier-based cell cultures are best suited to meet future demand of cytotherapies as they produce higher cell density and yield while better mimicking the in vivo microenvironment compared to monolayer cultures. The standard visualization methods used to monitor and analyze monolayer cell cultures do not readily translate to 3D microcarrier-based cultures and require the destructive detachment of cells from the microcarrier surface. We demonstrate non-destructive volumetric imaging and automated image analysis for quantitative evaluation cell count, culture confluency, and cell morphology of MSCs attached to microcarriers.

Dr. Kristen Maitland is an Associate Professor of Biomedical Engineering and the Director of the Microscopy and Imaging Center at Texas A&M University. Dr. Maitland’s research focuses on the development of light-based technologies for biomedical applications. Technologies include fiber-based imaging systems, endomicroscopes, handheld microscopes, volumetric imaging systems, portable spectrometers, and point-of-care devices. She received the NSF CAREER Award, TEES Select Young Faculty Award, Tenneco Meritorious Teaching Award, and William Keeler Memorial Award for outstanding contributions to the field of engineering. Dr. Maitland is a Fellow of the American Institute for Medical and Biological Engineering (AIMBE) and SPIE – the international society for optics and photonics.

Dr. Maitland serves on the Editorial Boards of SPIE Journal of Biomedical Optics and PLOS ONE and is the Biomedical Imaging Section Editor for Current Opinion in Biomedical Engineering. She serves on multiple conference program committees including as Chair of the 2022 Gordon Research Conference on Optics and Photonics in Medicine and Biology and the SPIE Multiscale Imaging and Spectroscopy Conference.

Dr. Maitland received her B.S. and M.S degrees in Electrical Engineering from Cal Poly, San Luis Obispo, and Ph.D. degree in Biomedical Engineering from The University of Texas at Austin as an NSF IGERT Research Fellow. Before joining the faculty at Texas A&M University in 2008, she was a Staff Scientist at Lawrence Livermore National Laboratory.

Component dynamics and realistic force balance allow particle-based simulations to recapitulate in vivo actomyosin ring kinetics.


Cytokinesis, the physical separation of one cell into two, occurs via the assembly and contraction of an actomyosin ring. While the parts list of the cytokinetic ring is well established, how the conserved cytoskeletal components rearrange, compact, and disassemble is poorly understood. One way we are working to understand mechanisms of contractile cytoskeletal remodeling is via particle-based modeling, which makes predictions about the relationships between network composition and contractility. Our contributions to date have focused on increasing the realism of simulations by optimizing the modeling of non-muscle myosin II (NMMII) ensembles and considering the forces that oppose ring closure. When a given amount of each component is set at the beginning of simulations and does not change, contractile kinetics do not recapitulate measurements of cytokinesis in vivo. Thus, in ongoing work, we are determining the abundance dynamics of primary structural elements by imaging fluorescently tagged ring components over the course of cytokinesis. To avoid photobleaching and the illumination of potentially fluorescent molecules outside the division plane, we developed a PDMS microfluidic device to position C. elegans zygotes upright such that the contractile ring forms in plane with a high N.A. objective light sheet. Raw image sequences were segmented with the use of deep learning, and contractile ring component intensity was measured over the length of cytokinesis. Component dynamics were incorporated into agent-based models of 3-dimensional contractile rings coupled to and exerting force on a deformable boundary representing the plasma membrane. When measured protein abundance was incorporated into simulations, rings closed with kinetics closely resembling that of in vivo rings. When measured dynamics were implemented for single core components (actin-like fibers, NMMII-like motor ensembles, anillin-like scaffolds, and septin-like membrane anchors), network dynamics still poorly recapitulated kinetics of biological rings, except for when the motor ensemble abundance was tuned. Our simulations demonstrate that not only the starting levels, but also dynamic abundance, of core structural components influence contractile ring kinetics. Furthermore, NMMII abundance has the most prominent influence on ring kinetics. Thus, our quantitative in vivo cell biology has refined our particle-based modeling and its predictive power for understanding how rings are built and remodeled to produce force and change cell shape

Dr Amy Shaub Maddox, a Professor of Biology at the University of North Carolina at Chapel Hill, leads a diverse team of researchers to understand the molecular mechanisms of cell shape stability and dynamics. Cytokinesis, the physical division of one cell into two, is driven by a highly dynamic ring of cellular polymers, motors and crosslinkers (collectively called the cortical cytoskeleton). These same cellular machines are also enriched on the stable rings that maintain structure and communication in syncytia, which are massive cells containing multiple nuclei. Many cells do cytokinesis, when they make a copy of themselves. Syncytia are common throughout nature, especially in the tissues that generate sperm and egg cells. How the cortical cytoskeleton remodels to define cell shape is poorly understood. The Maddox lab uses cell and developmental biology, genetics, biochemistry, computer-aided image processing, and computational modeling to study cytokinesis and syncytia. Ongoing work includes uncovering the cell and developmental mechanisms of septins, comparative studies of actomyosin rings in the germline syncytium, defining the regulatory and structural bases for contractile oscillations during cytokinesis, and testing the impact of cytokinetic ring protein dynamics on contractile kinetics. The team also places significant emphasis on teaching and outreach to a variety of audiences from grade school children, undergraduate students, and primary school teachers. We devise novel techniques to stimulate interdisciplinary interactions, including lunchMatrix, a program for increased networking via randomized informal meetings. Amy's overall goals are to facilitate discovery and fulfillment at the level of the individual, team, organization, and community.


Dr. Watkins has been a faculty at the University of Pittsburgh since he joined as an Assistant Professor in 1991 from the Dana Farber in Boston. He is now a distinguished Professor of Cell Biology and Professor of Immunology. He is the founder and director of the Center for Biologic Imaging at the University of Pittsburgh, which is in internationally renowned intellectual nexus for the application of all aspects of microscopic imaging specifically for the study of molecular, cellular and tissue biology. He has been successful in nurturing the Center from infancy to a highly productive (35+papers/year), well funded organization employing 25 people including, faculty, postdoctoral fellows and research specialists and students. Currently the Center collaborates with over 300 groups within the University and around the world each year. Dr Watkins has authored close to 700 peer reviewed papers (H index 141) and has co-edited a book in the principles and application of high-end biomedical microscopy and image analysis. He teaches courses on microscopy both within our institution and nationally and chairs or serves on multiple NIH panels each year, he is also a member of the research council for the American Cancer Society and a member of the University of Pittsburgh Cancer Institute.

Considerations for processing large data with python and napari'


Will discuss napari, a fast, interactive, multi-dimensional image viewer for Python. napari is designed for browsing, annotating, and analyzing large multi-dimensional images. We will cover the basic principles and interface of napari, with an emphasis on how napari helps with visualization of large, out-of-core datasets as are typically generated with light sheet microscopy. We'll also briefly discuss extending napari with plugins.

Talley Lambert is a microscopist and python developer at Harvard Medical School.

Optical Sectioning and basic fluorescence microscopy


This presentation will cover a brief introduction to fluorescence microscopy and various methods that can be used to produce optical sectioning, or removal of out-of-focus light.

Dr. Itano is a cellular biophysicist, Assistant Professor of Cell Biology and Physiology and Director of the UNC Neuroscience Microscopy Core, where she develops and customizes state-of-the-art optical imaging and analysis applications for a wide range of scientific research. She utilizes innovative fluorescence microscopy methods—including super-resolution and simultaneous multi-plane imaging—to investigate how viruses, such as HIV-1, infect cells.

How the embryo gets its shape: understanding early mouse development with light-sheet microscopy


Development begins with a single cell of limitless potential giving rise to all of the different cell types, tissues, and organ systems that comprise an adult animal. How cells organize to build tissues and how those tissues are sculpted to form organs however, is largely unknown. As mammalian embryos are highly sensitive to environmental and culture conditions, and in addition are extremely photosensitive, visualizing their development has been notoriously difficult. We have developed an advanced light-sheet microscope to gently and comprehensively image mouse embryo development at single-cell resolution over a course of days. With this system and a suite of computational tools, we can track individual cells and analyse patterns of divisions, as well as build dynamic cell fate maps over the course of two-days of development from gastrulation to early organogenesis. This allows us to describe the morphogenesis of complex three-dimensional structures such as the formation of the early heart, the neural tube, node and notochord, and the formation of the primitive streak.

Kate McDole is a newly appointed Group Leader at the MRC Laboratory of Molecular Biology in Cambridge, UK. Her lab explores the morphogenesis of the early mouse embryo using a combination of advanced light-sheet microscopy, biology, computational methods and biophysics. Kate did her PhD at Johns Hopkins at the Carnegie Institute for Science’s Department of Embryology in the lab of Yixian Zheng, using two-photon microscopy to study early cell fate establishment in the pre-implantation mouse embryo. She moved to HHMI’s Janelia Research Campus to do her post-doc in the lab of Philipp Keller, developing a light-sheet microscope for imaging post-implantation mouse development.

High-Resolution Oblique Plane Microscopy


We present a high-resolution oblique plane microscope (OPM) that improves the resolution and field of view over previous light-sheet microscopes, but in a user-friendly inverted geometry that is compatible with standard sample preparation, environment control, and hardware-based autofocusing technologies. Given its performance, we demonstrate high-resolution sub-cellular imaging of endocytosis, intermediate filaments, organelles, and formation of the immunological synapse. We also image many phenomena that would be otherwise challenging to observe in a traditional light-sheet microscope geometry such as the subcellular photoactivation of Rac1, cell migration through a microfluidic device, developing embryos, and single molecule fluorescence in-situ hybridization in centimeter-scale tissue sections. More recently, to improve the speed and versatility of the imaging system, we augmented it with a novel detection technology that allows one to acquire projections of the specimen from multiple perspectives with uncompromised spatial resolution and image contrast. Using this approach, the temporal resolution of the imaging system is limited only by the camera framerate and the specimen’s emitted photon flux, thereby allowing us to image action potentials in cultured neurons at rates up to 119 Hz. Furthermore, by rapidly imaging specimens from multiple perspectives, we can tomographically reconstruct the original image volume an order of magnitude faster than traditional light-sheet microscopy approaches. By interleaving the projection angle, or adding a second camera, we can even operate the microscope in a real-time stereoscopic virtual reality mode. This opens entirely new opportunities in fluorescence imaging, for which we have only scratched the surface.

Kevin Dean was raised in a small town in Northern California and received his B.A. in Chemistry at Willamette University in Oregon, where he was recognized twice as an ESPN Regional Academic All-American. After college, he raised money and awareness for Amyotrophic Lateral Sclerosis, which is more commonly known as Lou Gehrig’s Disease, by riding a bicycle across the United States with two close friends. He then moved to the Rocky Mountains and received his Ph.D. in Biochemistry at the University of Colorado under the guidance of Dr. Amy Palmer and Dr. Ralph Jimenez. Here, his work focused on spectroscopy, protein engineering, and multi-parameter high-throughput microfluidic analyses and cell sorting. During this time, he also established the first campus-wide light microscopy facility at the BioFrontiers Institute. Thereafter, he moved to the University of Texas Southwestern Medical Center in Dallas to perform his postdoctoral research under the guidance of Dr. Gaudenz Danuser and Dr. Reto Fiolka, where he was named a Ruth L. Kirschstein Postdoctoral Fellow, received the Dean’s Discretionary Award at UT Southwestern, and was the runner-up for the UTSW Brown-Goldstein Excellence in Postdoctoral Research award. Today, he runs a collaborative lab at UTSW that seamlessly integrates cutting-edge computer vision, microscopy, and biology to identify the molecular mechanisms that enable cancer cells to colonize and populate distant tissues.

Adaptive optics for high-resolution microscopy


The past quarter century has witnessed rapid developments of fluorescence microscopy techniques that enable structural and functional imaging of biological specimens at unprecedented depth and resolution. The performance of these methods in multicellular organisms, however, is degraded by sample-induced optical aberrations. Here I review our recent work on incorporating adaptive optics, a technology originally applied in astronomical telescopes to combat atmospheric aberrations, to improve image quality of fluorescence microscopy for biological imaging.

Na Ji received her B.S. in Chemical Physics from the University of Science & Technology of China in 2000. She received her Ph.D. in Chemistry from the University of California, Berkeley in 2005, working in the laboratory of Yuen-Ron Shen. She moved to the Janelia Research Campus, Howard Hughes Medical Institute for her postdoctoral training with Eric Betzig in 2006. She became a Group Leader at Janelia Research Campus in 2011. She returned to Berkeley and joined the Physics and Molecular & Cell Biology Departments in 2016. She is currently the Luis Alvarez Memorial Chair in Experimental Physics and an associate professor of neurobiology.

Lattice light sheet microscopy – innovations, applications and future directions


Living specimens are both animate and three-dimensional. Lattice Light Sheet Microscopy (LLSM) utilizes optically structured beams to perform fast 3D imaging of dynamic processes in vivo with improved resolution and beam uniformity. I will provide an overview and characterization of different types of lattice lightsheet beams and their respective advantages and tradeoffs for live-cell imaging. I will also discuss our recent work developing lightsheet compatible microfluidic chips, AI-based instrument control algorithms, and single molecule imaging applications.

Dr. Legant is a joint assistant professor in the departments of Biomedical Engineering and Pharmacology at the University of North Carolina – Chapel Hill. His lab develops new optical imaging techniques and image analysis tools. The lab is currently applying these new tools to understand diverse biological processes ranging from cell migration to gene transcription. Prior to joining UNC, Dr. Legant was a research scientist at HHMI Janelia Research Campus, where he worked together with Eric Betzig to develop and apply novel light microscopy technologies including Lattice Light Sheet; super resolution structured illumination and single molecule localization microscopy; and adaptive optics for fundamental applications in cell biology. Dr. Legant received his PhD in Bioengineering from the University of Pennsylvania and a BS in Biomedical Engineering from Washington University in St. Louis.

A modular approach to tissue clearing


Tissue clearing of gross anatomical samples was first described over a century ago and has recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Unfortunately, the current literature is complex and confusing to researchers looking to begin a clearing project. Here, we outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest.

Doug received his PhD from the Department of Pathology and Molecular Medicine at Queen’s University (Canada) in the field of cancer cell biology. Following his graduate studies, he continued to refine his skills as an Alexander von Humboldt post-doctoral fellow in the lab of Professor Stefan Hell (Nobel Prize in Chemistry, 2014).  Currently, Doug is the Director of Imaging at the Harvard Center for Biological Imaging, and a Lecturer in Harvard’s Department of Molecular and Cellular Biology.  Doug investigates, evaluates and teaches a wide range of light microscopy techniques and image processing methodologies.

Hyperspectral light sheet microscopy for 5D imaging of living tissues.


Our understanding of cellular dynamics has been advanced significantly by live-cell fluorescence microscopy experiments. Live-cell hyperspectral imaging permits simultaneous measurements of multiple dynamic processes with excellent signal-to-noise ratios. We have developed a novel five-dimensional (x,y,z,t,λ) fluorescence imaging system that provides high spatial, temporal, and spectral resolution with minimal photobleaching. This instrument combines dual-view Selective-Plane Illumination Microscopy (diSPIM) that yields isotropic diffraction-limited imaging and image mapping spectroscopy (IMS) that permits single snapshot hyperspectral imaging of multiple fluorophores with a single excitation wavelength. We have developed and optimized this system using the islet of Langerhans, a micro-organ that contributes to blood glucose homeostasis through the regulated secretion of glucagon (from α-cells) and insulin (from β-cells). The molecular processes underlying secretion of these hormones secretion are captured using light sheet microscopy, with its intrinsic optical sectioning, fast acquisition of three-dimensional data sets, and low photobleaching. To visualize multiple probes in this rapid acquisition environment, a snapshot hyperspectral method is required, and we demonstrate the efficacy of the IMS in this system. We show that this approach permits distinguishing α- from β-cells in an intact islet, while simultaneously acquiring cellular dynamics data. We are measuring intracellular dynamics of insulin vesicle trafficking and secretion to test the hypothesis that “readily releasable” and “reserve” vesicle pools lead to the observed two phases of glucose-stimulated insulin secretion. We are correlating vesicle movements to microtubules and actin fibers, and measuring the regulation of these movements are regulated by intracellular free calcium activity and cAMP levels.

David W. Piston is the Edward J. Mallinckrodt Jr. Professor and Head of the Department of Cell Biology and Physiology, Professor of Physics, and Professor of Bioengineering at Washington University in St. Louis. Dr. Piston received a BA from Grinnell College, followed by M.S. and Ph.D. degrees in Physics at the University of Illinois. His doctoral dissertation work was done under the mentorship of Prof. Enrico Gratton, and he subsequently completed a postdoctoral research fellowship in Applied Physics with Watt Webb at Cornell University. In 1992, Dr. Piston joined the faculty at Vanderbilt University, where he remained until the end of 2014, when he moved to Washington University. He has received a number of honors including a Beckman Young Investigator Award (1993), NIH Study Section Chair (2004-2006), Searle Scholars Advisory Board (2006-20112), election as a Fellow of the American Physical Society (2000), the Microscopy Society of America (2014), the American Association for the Advancement of Science (2015), and the Distinguished Scientist Award from the Microscopy Society of America (2017). Dr. Piston has a long history of inventing new fluorescence spectroscopy and microscopy approaches, and applying them to open questions about biological mechanisms.

Practical Aspects of Objective Lens Design

Cover aberrations, lens types, specifications, etc. also cover lenses for light sheet, but as techniques broaden, the old key specifications of cone angle, WD, etc. are not critical for all geometries.

Steve Ross is the Director of Product & Marketing for NIKON Instruments Inc.

3D single-molecule tracking and super-resolution imaging throughout cells using a tilted light sheet


Cellular function is governed by the organization of nanoscale structures and by molecular interactions within and between cells. In this talk, I will present our microscopy platforms where we combine light sheet illumination with point spread function engineering to achieve 3D single-molecule tracking and super-resolution imaging with tens of nm precision throughout mammalian cells. Our tilted light sheet designs optically section the cells to reduce fluorescence background, photobleaching, and the risk of photodamaging live cells, while allowing imaging of entire adherent cells all the way from the coverslip and up. I will demonstrate applications where we have utilized these platforms to provide structural details of the nuclear lamina, sugars in the glycocalyx and how they are modulated during cancer progression, and of previously unknown structures in the inversin compartment in primary cilia. I will also showcase how they can be applied for 3D tracking of chromatin dynamics over time scales ranging from milliseconds to hours, and length scales ranging from nanometers to micrometers. In summary, our imaging platforms are versatile and can be utilized to study a variety of cellular nanoscale structures, dynamics, and molecular mechanisms. We think they will continue to be useful for answering a wide range of biological and biomedical questions related to cellular function and pathogenesis.

Dr. Gustavsson joined the faculty at Rice University in the summer of 2020 as a CPRIT Scholar and the Norman Hackerman-Welch Young Investigator Chair. Her research group strives to gain detailed information about cellular nanoscale structure, dynamics, and molecular mechanisms by designing and applying innovative and versatile imaging tools. The goal of their research is to improve our understanding of cellular function and pathogenesis to answer biophysical and biomedical questions related to aging, cancer, and other diseases. Dr. Gustavsson received her PhD in Physics from the University of Gothenburg, Sweden, in 2015. Her work focused on studying dynamic responses in single cells by combining and optimizing techniques such as fluorescence microscopy, optical tweezers, and microfluidics. Upon completion of her graduate work, Dr. Gustavsson joined the group of Nobel Laureate W. E. Moerner at Stanford University as a Postdoctoral Fellow in 2015. Her research focused on the development and application of 3D single-molecule super-resolution microscopy for cellular imaging and included the implementation of light sheet illumination for optical sectioning of mammalian cells. Dr. Gustavsson’s work has been recognized with multiple honors, awards, and fellowships, most notably the FEBS Journal Richard Perham Prize for Young Scientists in 2012, the 3-year Swedish Research Council International Postdoc Fellowship in 2016, the PicoQuant Young Investigator Award in 2018, the NIH K99/R00 Pathway to Independence Award in 2019, the CPRIT Recruitment of First-Time Tenure-Track Faculty Members Award in 2020, and the Scialog: Advancing Bioimaging Fellowship in 2021.

Uncovering cell dynamics in developing embryos, embryoids and organoid models


Recent trends in developmental biology and clinical research have introduced a variety of embroid and organoid models that resemble the in vivo 3D environment. However, these models are extremely sensitive to the imaging environment and are more variable in their morphology as compared to embryos/organs. Hence, a larger sample size is required to obtain a reliable understanding of the system, posing challenges in terms of imaging throughput, data handling, visualization of numerous big datasets and integration of information therein. We are addressing these by implementing robust incubation systems and multi-sample imaging and analysis pipelines. I will discuss our recent efforts in addressing these in many biological systems including time-lapse imaging of tissue derived organoids, embryos as well as of embryoid models derived from zebrafish and mouse embryonic stem cells which recapitulate events from embryonic development. 

Gopi Shah is the Project Manager for Advanced Mesoscopy Applications at the Mesoscopic Imaging Facility (MIF) in EMBL Barcelona. MIF provides imaging and data processing services for large, chemically cleared as well as live biological tissues with commercial and custom implementations of microscopy and tomography techniques.

Gopi obtained her PhD from the Max Planck Institute for Cell Biology and Genetics (MPI-CBG) in Dresden, Germany, where she worked on developing light sheet microscopes capable of long-term, high-throughput imaging and real-time data processing. Thereafter, she joined the Cancer Research UK Cambridge Institute (CRUK CI) in Cambridge, where she established light sheet microscopy as a tool for imaging various tumour-derived organoid and co-culture models to observe tumor biology in 4D. Her current work at EMBL focuses on enabling live imaging of a variety of in vitro 3D models of animal development and diseases in collaboration with scientists at EMBL and beyond. Broadly, she has been working on designing imaging infrastructures that enable scientists to seamlessly acquire, analyse and visualise large-scale bioimaging data.