Abstract

In recent years, single-cell data visualization has primarily focused on dimensionality reduction techniques and scatter plots. However, with the advent of spatial single-cell biology, the demand for interactive tools supporting visual exploration of integrated, multi-modal spatial datasets has surged. These datasets often encompass measurements of multiple molecular entities and are generated using diverse assays. To address the rapidly evolving landscape of data sets and analytical tools, we have developed the Vitessce visualization framework (http://vitessce.io). This talk will introduce the Vitessce framework, highlighting its capabilities and applications across various research studies and software tools. Additionally, the talk will outline the key challenges associated with visualizing spatial biology data and propose a research agenda that integrates visual and computational approaches. By attending this talk, researchers and practitioners will gain insights into the latest advancements in single-cell data visualization, enabling them to leverage the power of the Vitessce framework for their own studies.

Biography

Nils Gehlenborg, PhD, 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. In addition to his research role, he is Director of the Master in Biomedical Informatics program and Director of the NIH-funded Biomedical Informatics and Data Science Research Training (BIRT) program. Nils also co-chairs the Diversity, Equity, and Inclusion (DEI) Committee at Harvard Medical School. 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. Tight 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. His efforts methods are designed to support sense-making in biology and medicine and to support reproducible, collaborative research. Nils was a predoctoral fellow at the European Bioinformatics Institute (EMBL-EBI) and received his PhD from the University of Cambridge in 2010. He completed his postdoctoral training as a Research Associate in the Center for Biomedical Informatics at Harvard Medical School in 2015. 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. Nils has served on the program committees of several international bioinformatics and data visualization conferences and held multiple editorial roles, including his current role as associate editor of BMC Bioinformatics. He has also contributed to the “Points of View” data visualization column in Nature Methods.