Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

Events on March 20, 2023

Robert Krueger

Robert Krueger, Postdoc Research Fellow at VGC Harvard Presents:

From Visual Analytics to Data-Driven Communication of Large Biomedical Cancer Images

March 20, 2023 at 10:00am for 1hr
Evans Conference Room, WEB 3780
Warnock Engineering Building, 3rd floor.

Zoom: Passcode: 090406


With new tumor imaging technology, cancer biology is undergoing a transformation into a digital era. Artificial intelligence has enabled processing and analysis of the resulting datasets of unprecedented scale. However, expert involvement and human domain knowledge are still essential, as data acquisition and experimental analysis pipelines are rapidly evolving. In my talk, I will present a scalable rendering framework enabling users to load, display, and interactively navigate in terabyte-sized multiplexed images of cancer tissue. I will then present visual analytics interfaces that utilize this framework and integrate machine learning methods to support cell biologists and pathologists in their workflows. The first step in such a workflow is a semi-automatic data filtering procedure, called "gating", which improves data quality and is critical for downstream analysis. I will then discuss the integration of unsupervised and supervised learning to identify stromal, immune, and cancer cells at scale. Subsequently, neighborhoods of cells are quantified in order to query and cluster repetitive and biologically-meaningful interaction patterns. Once relevant patterns are identified, a focus and context interface allows pathologists to further assess and annotate these regions of interest in an intuitive fashion. To communicate the biomedical insights to the greater research community and educate students, the findings and annotations can be extracted and arranged into interactively guided data stories. I will conclude with an outlook into my future research agenda addressing the transition to volumetric and time-varying datasets, and the joint analysis of multimodal images and increasing amounts of spatially-referenced high-dimensional data.

Dr. Robert Krueger is a Postdoctoral Research Scientist at Harvard University with a shared appointment between the Visual Computing Group at the School of Engineering and Applied Sciences and the Laboratory of Systems Pharmacology at Harvard Medical School. In this setting, Dr. Krueger leads a subgroup for biomedical visual computing focusing on visualization and computer vision approaches for cancer research, in close collaboration with pathologists, biologists, and oncologists. Dr. Krueger's interdisciplinary research centers on designing and developing visual interfaces for the exploration, analysis, and communication of large and multiplexed imaging data. His research has been published in primary venues such as IEEE VIS, IEEE Transaction on Visualization and Computer Graphics (TVCG), and Computer Graphics Forum (CGF), and his approaches have contributed key elements to biomedical publications in Cancer Cell and Nature Biomedical Engineering. Before joining Harvard, Dr. Krueger received his Ph.D. in Computer Science from the University of Stuttgart, Germany where he worked on geographical visualization and visual analytics methods including traffic, mobility, and social media analysis.

Posted by: Deb Zemek

Gia-Bao Ha Presents:

March 20, 2023 at 12:00pm for 30min
Evans Conference Room, WEB 3780
Warnock Engineering Building, 3rd floor.

Posted by: Mitra Alirezaei