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Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…

Quantitative Methods · Quantitative Biology 2024-05-06 Ajit J. Nirmal , Peter K. Sorger

There is a strong demand for virtual reality (VR) to bring quality healthcare to underserved populations. This paper addresses this need with the design and prototype of SURVIVRS: Surround Video-Based Virtual Reality for Surgery Guidance.…

Human-Computer Interaction · Computer Science 2023-05-05 Amani Taweel , Joaquim Jorge , Anderson Maciel , João Ricardo Nickenig Vissoci , Regis Kopper

Microbiome studies have recently transitioned from experimental designs with a few hundred samples to designs spanning tens of thousands of samples. Modern studies such as the Earth Microbiome Project (EMP) afford the statistics crucial for…

Genomics · Quantitative Biology 2021-11-02 Igor Sfiligoi , Daniel McDonald , Rob Knight

Virtual reality (VR) offers immersive visualization and intuitive interaction. We leverage VR to enable any biomedical professional to deploy a deep learning (DL) model for image classification. While DL models can be powerful tools for…

Machine Learning · Computer Science 2022-06-22 Kevin C. VanHorn , Meyer Zinn , Murat Can Cobanoglu

We propose VRGym, a virtual reality testbed for realistic human-robot interaction. Different from existing toolkits and virtual reality environments, the VRGym emphasizes on building and training both physical and interactive agents for…

Human-Computer Interaction · Computer Science 2019-04-04 Xu Xie , Hangxin Liu , Zhenliang Zhang , Yuxing Qiu , Feng Gao , Siyuan Qi , Yixin Zhu , Song-Chun Zhu

Timelines are common visualizations to represent and manipulate temporal data, from historical events storytelling to animation authoring. However, timeline visualizations rarely consider spatio-temporal 3D data (e.g. mesh or volumetric…

Human-Computer Interaction · Computer Science 2022-06-22 Gwendal Fouché , Ferran Argelaguet , Emmanuel Faure , Charles Kervrann

Tangible interfaces in mixed reality (MR) environments allow for intuitive data interactions. Tangible cubes, with their rich interaction affordances, high maneuverability, and stable structure, are particularly well-suited for exploring…

Human-Computer Interaction · Computer Science 2024-03-12 Shuqi He , Haonan Yao , Luyan Jiang , Kaiwen Li , Nan Xiang , Yue Li , Hai-Ning Liang , Lingyun Yu

Robotic manipulation requires understanding both the 3D spatial structure of the environment and its temporal evolution, yet most existing policies overlook one or both. They typically rely on 2D visual observations and backbones pretrained…

Confronted by a rapidly evolving health threat, such as an infectious disease outbreak, it is essential that decision-makers are able to comprehend the complex dynamics not just in space but also in the 4th dimension, time. In this paper…

We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus,…

Quantitative Methods · Quantitative Biology 2022-10-04 Pavol Ulbrich , Manuela Waldner , Katarína Furmanová , Sérgio M. Marques , David Bednář , Barbora Kozlikova , Jan Byška

One of today's most propitious immersive technologies is virtual reality (VR). This term is colloquially associated with headsets that transport users to a bespoke, built-for-purpose immersive 3D virtual environment. It has given rise to…

Human-Computer Interaction · Computer Science 2019-10-23 Slawomir Konrad Tadeja , Pranay Seshadri , Per Ola Kristensson

Virtual laboratories are the new online educational trend for communicating to students practical skills of science. In this paper we report on a comparison of techniques for familiarizing distance learning students with a 3D virtual…

Human-Computer Interaction · Computer Science 2017-12-01 Evgenia Paxinou , Vasilis Zafeiropoulos , Athanasios Sypsas , Chairi Kiourt , Dimitris Kalles

Microbial networks, representing microbes as nodes and their interactions as edges, are crucial for understanding community dynamics in various environments. Analyzing microbiome networks is crucial for identifying keystone taxa that play…

Molecular Networks · Quantitative Biology 2025-07-15 Qiyao Yang , Rosa Aghdam , Reed Nelson , Claudia Solís-Lemus

Live time-lapse microscopy is essential for a wide range of biological applications. Software-based automation is the gold standard for the operation of hardware accessories necessary for image acquisition. Given that current software…

Image and Video Processing · Electrical Eng. & Systems 2019-06-20 Quang Long Pham , David Chege , Timothy Dijamco , Migle Surblyte , Akshay Naik , Kolawole Campbell , Nhat-Anh-Nguyen Tong , Roman Voronov

Molecular dynamics (MD) simulations are a crucial computational tool for researchers to understand and engineer molecular structure and function in areas such as drug discovery, protein engineering, and material design. Despite their…

Multimodal research and applications are becoming more commonplace as Virtual Reality (VR) technology integrates different sensory feedback, enabling the recreation of real spaces in an audio-visual context. Within VR experiences, numerous…

Audio and Speech Processing · Electrical Eng. & Systems 2025-04-08 Mauricio Flores-Vargas , Enda Bates , Rachel McDonnell

Understanding and predicting microstructure evolution is fundamental to materials science, as it governs the resulting properties and performance of materials. Traditional simulation methods, such as phase-field models, offer high-fidelity…

Machine Learning · Computer Science 2026-02-24 Michael Trimboli , Mohammed Alsubaie , Sirani M. Perera , Ke-Gang Wang , Xianqi Li

We introduce SigmaCollab, a dataset enabling research on physically situated human-AI collaboration. The dataset consists of a set of 85 sessions in which untrained participants were guided by a mixed-reality assistive AI agent in…

Human-Computer Interaction · Computer Science 2025-11-05 Dan Bohus , Sean Andrist , Ann Paradiso , Nick Saw , Tim Schoonbeek , Maia Stiber

We propose manvr3d, a novel VR-ready platform for interactive human-in-the-loop cell tracking. We utilize VR controllers and eye-tracking hardware to facilitate rapid ground truth generation and proofreading for deep learning-based cell…

Human-Computer Interaction · Computer Science 2026-01-06 Samuel Pantze , Jean-Yves Tinevez , Matthew McGinity , Ulrik Günther

We propose and study a novel cross-reality environment that seamlessly integrates a monoscopic 2D surface (an interactive screen with touch and pen input) with a stereoscopic 3D space (an augmented reality HMD) to jointly host spatial data…

Human-Computer Interaction · Computer Science 2024-09-25 Lixiang Zhao , Tobias Isenberg , Fuqi Xie , Hai-Ning Liang , Lingyun Yu