Challenges and Opportunities in Visualization of 3D Spatial and Single-Cell Data
Talk by Nils Gehlenborg, Harvard Medical School, Department of Biomedical Informatics
Date: Monday, June 24th 2024, 11:00- 12:00
Where: SR6 (1st floor), Währinger Straße 29, 1090 Vienna
Online Zoom Link: https://univienna.zoom.us/j/65940635874?pwd=HBQmoZElWQBNmVnb4B7bMtDYRGPHKs.1
Single-cell data visualization was for a long time focused on the application of dimensionality reduction techniques and scatters plots. The emergence of spatial single-cell biology, however, rapidly created a need for interactive tools that support visual exploration of integrated, multi-modal spatial datasets. These datasets often include measurements of multiple molecular entities and are generated using diverse assays. To address this quickly evolving landscape of data sets and analytical tools, we developed the Vitessce (http://vitessce.io) visualization framework. This talk will introduce the framework and its capabilities as well as its applications in a wide range of research studies and software tools. Finally, the talk will outline the key challenges associated with visualizing 3D spatial biology data and outline a research agenda that integrates visual and computational approaches.
Bio:
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. Nils is a co-founder and advisor of Datavisyn, which is a company that provides visualization solutions for applications in pharmaceutical and biomedical R&D.
