Application Spotlights

Accepted Application Spotlights

Below you will find the 2023 accepted Spotlight. If you have any questions about the spotlight session, please contact the organizers listed below directly.

Visualization for spatial single-cell atlases: Identifying challenges and opportunities in complex biomedical data at multiple scales and modalities

When: Thursday, October 26, 2023 10:45 AM-12:00 PM AEDT (UTC+11)
Location: Room 101+102

Organizers

Morgan Turner, Harvard Medical School, Boston, USA Eric Moerth, Harvard Medical School, Boston, USA Nils Gehlenborg, Harvard Medical School, Boston, USA

Summary

Technological advances in biological experimental approaches for studying human tissues at single-cell resolution are producing large amounts of complex data and are offering new ways to ask questions with far-reaching impacts on human health. To allow for comprehensive analysis and comparison of the generated data, the ultimate goal is to construct an atlas of the human body that characterizes the cell types, tissue structures, and abundance of different types of biomolecules across these structures. The data supporting these atlas efforts, however, is creating challenging visualization problems due to 1) the dimensionality and density of the data and 2) the multi-modal measurements (including proteins, genes, and metabolites) associated with these structures in both 2D images and 3D volumes. Additionally, many datasets routinely include tens of thousands to millions of cells, with up to thousands of measurements per cell, resulting in critical scalability challenges.

This new paradigm of tissue atlas construction presents many relevant visualization challenges that will require the visualization community’s expertise to address. Due to the inherent anatomical nature of the data, biologists need to interact with this data in spatial and hierarchical contexts using visualization systems that are able to handle multi-modal visualization and queries at scale. Particularly in the context of diseases, visualizations are required to allow for comparisons of normal vs. disease, context of other biomedical information, display of uncertainty, and tools for education and training. Some of these visualization efforts have already been applied to cancer and kidney disease and are having impacts on research in human health.

We aim to identify future avenues of visualization research that can be helpful for exploring and analyzing data within these cell atlases. Augmented Reality (AR), and Virtual Reality (VR) offer potential for navigation and data analysis in 3D, but require careful consideration of useful techniques for users. Additionally, Artificial Intelligence (AI) approaches are being employed and will require explainable/interpretable visualization techniques. We plan to focus part of the panel discussion on the advantages and opportunities of employing these visualization technologies to aid in our understanding of human biology and aim to identify worthwhile future directions for visualization research to target.

Schedule

Opening: Eric Moerth (5 min) Panelist presentations (total: 40 min)

  • Ajay Pillai: HuBMAP and related Cell Atlas efforts (10 min)
  • Mark Keller: Vitessce: Visual integration tool for exploration of spatial single-cell experiments (10 min)
  • Barbora Kozlíková: 3D structural biology data (10 min)
  • Stefan Bruckner: Volumetric Rendering of Medical Imaging data and how to translate it in AR/VR (10 min) Panel Q&A Moderators: Nils Gehlenborg and Morgan Turner (25 min) Closing: Eric Moerth (5 min)

Speakers

Ajay Pillai - Dr. Ajay Pillai joined the National Human Genome Research Institute’s Extramural Research Program as program director in 2006. He manages a portfolio of grants focused on data and knowledge resources, single cell biology, AI/ML methods development including approaches to development of ethical AI, and other computational approaches. He co-leads two Common Fund programs: HuBMAP (single-cell mapping of “normal” human tissue and organs) and IDG (developing computational and experimental reagents to study under-studied proteins). He co-leads a trans-NIH effort on developing and sustaining data and knowledge resources. He also co-leads a new NHGRI program, MorPhiC (Molecular Phenotypes of Null Alleles in Cells), that aims in the long-term to develop a consistent catalog molecular and cellular phenotypes for null alleles for every human gene by using in-vitro multicellular systems. https://www.genome.gov/staff/Ajay-Pillai-PhD

Mark Keller - Mark Keller is a PhD student in the Bioinformatics and Integrative Genomics Program at Harvard Medical School. Previously, he was a software developer with a B.S. in Computer Science from the University of Maryland and a former intern in the Summer Institute in Biomedical Informatics in the Gehlenborg Lab. Mark is the lead software developer on Vitessce: Visual integration tool for exploration of spatial single cell experiments. https://markk.co/ http://vitessce.io/

Barbora Kozlíková - Dr. Barbora Kozlíková is an Associate Professor at the Faculty of Informatics, Masaryk University, Brno, Czech Republic. She is a member of the Department of Visual Computing and is also heading the Visitlab research group focusing on diverse topics in visualization. Bara got her Ph.D. in Computer Graphics in 2011 and her main research interests are visualization and visual analysis with diverse application areas, including biochemistry, medicine, geography, and criminology. With her 7 Ph.D. students she is working on many interesting research topics. She is also responsible for several courses taught at her faculty and is always interested in starting new collaborations. With her colleagues and friends, she is also organizing events for the community, e.g. the EG EuroVis 2018 conference and also the EG VCBM 2019 workshop. https://www.fi.muni.cz/~xkozlik/

Stefan Bruckner - Dr. Stefan Bruckner is a visualization researcher and professor at the University of Rostock, where he is the head the Chair of Visual Analytics at the Institute for Visual and Analytic Computing since February 2023. Previously, he was professor of visualization at the Department of Informatics of the University of Bergen in Norway. He investigates methods for gaining insight into complex data to further scientific understanding and discovery, medical diagnosis and treatment, and engineering, as well as techniques for communicating these findings to the public. Building on these foundations, his current interests include the development of novel interactive approaches for the inquiry of large-scale heterogeneous data spaces in data-driven science. Stefan was program co-chair of EuroVis, PacificVis, the Eurographics Workshop on Visual Computing for Biology and Medicine, the Eurographics Medical Prize, and is an associate editor of the journals IEEE Transactions on Visualization and Computer Graphics and Computers & Graphics. He currently serves on the Eurographics Executive Committee and is member of ACM SIGGRAPH, Eurographics, and the IEEE Computer Society.

Morgan Turner - Dr. Morgan Turner is an R&D Manager and Visualization Scientist in the Department of Biomedical Informatics at Harvard Medical School. She was previously a postdoctoral research associate and CRA/CCC/NSF Computing Innovation Fellow in the Interactive Visualization Lab at the University of Minnesota, focusing on developing visualization techniques for spatially- and temporally-referenced skeletal biomechanical data. Morgan received her PhD in Ecology and Evolutionary Biology at Brown University in 2021. During her PhD, she developed methods of visualizing 3D kinematic data generated from high-speed X-ray videography, as well as collaborated on the development of Virtual Reality visualizations for analyzing volumetric flow patterns of mud during dinosaur footprint formation. https://morganlturner.com/

Eric Moerth - Dr. Eric Moerth is a Postdoctoral Associate in the Department of Biomedical Informatics at Harvard Medical School. He received his PhD from the University of Bergen in Norway, under the supervision of Prof. Noeska Smit. During his PhD study, he conducted research in multimodal medical visualization. His main focus was the research of new and innovative ways to visualize and explore 3D biomedical data, e.g. MRI data and radiomics data. He also developed innovative tools for storytelling with guided dynamic narratives for scientific data. http://hidivelab.org/team/members/eric-moerth/

Nils Gehlenborg - Dr. Nils Gehlenborg is an Associate Professor in the Department of Biomedical Informatics at Harvard Medical School and directs the Humans in Data Integration, Visualization, and Exploration (HIDIVE) Lab (http://hidivelab.org). The goal of Nils’ research is to improve human health by developing visual interfaces and computational techniques that enable scientists, clinicians, and patients to efficiently interact with biomedical data. Integration of algorithmic and machine learning approaches from biomedical informatics with advanced data visualization techniques is central to his efforts, as is close collaboration with end users. Nils is a co-founder, former general chair and steering committee chair of BioVis, the Symposium on Biological Data Visualization, and co-founder of VIZBI, the annual workshop on Visualizing Biological Data.