1 citations · 1 across the 16 of their papers we have counts for
17 papers
How Do We Visualize Space in Molecular Biology? A Study of Spatial Transcriptomics Visualization Practices
Denisse Chacón-Ramírez, Mark S. Keller, Eric Mörth +3
A cell's identity depends on where it sits in tissue: for example, a macrophage behaves differently in a tumor core than at its edge. Spatial transcriptomics has transformed how we…
Agentic Authoring of Interactive Multiview Visualizations in Genomics
Astrid van den Brandt, Kiroong Choe, Sehi L'Yi +2
Diverse genomics data, scientific questions, and analysis tasks typically demand highly specialized visualizations. Therefore, users often must customize or author new ones tailore…
Pluot: Towards 'write once, run everywhere' visualization software
Mark S. Keller, Nils Gehlenborg
Tools used for implementing visualization software systems can generally be divided into camps such as static versus interactive and desktop versus web-based. We contribute Pluot,…
Sycamore: Characterizing Synthetic Personas for Evaluating Genomics Visualization Retrieval
Huyen N. Nguyen, Astrid van den Brandt, Nils Gehlenborg
Evaluating visualization systems in niche domains such as genomics is challenging due to scarcity of domain experts and difficulty recruiting a representative user base. While LLM-…
Visualization Retrieval for Data Literacy: Position Paper
Huyen N. Nguyen, Nils Gehlenborg
Current resources for data literacy education, such as visualization galleries and datasets, provide useful examples but lack mechanisms for learners to query, compare, and navigat…
Automatic Synthesis of Visualization Design Knowledge Bases
Hyeok Kim, Sehi L'Yi, Nils Gehlenborg +1
Formal representations of the visualization design space, such as knowledge bases and graphs, consolidate design practices into a shared resource and enable automated reasoning and…
Gosling Designer: a Platform to Democratize Construction and Sharing of Genomics Data Visualization Tools
Sehi L'Yi, John Conroy, Priya Misner +5
Analysis of genomics data is central to nearly all areas of modern biology. Despite significant progress in artificial intelligence (AI) and computational methods, these technologi…
Vitessce Link: A Mixed Reality and 2D Display Hybrid Approach for Visual Analysis of 3D Tissue Maps
Eric Mörth, Morgan L. Turner, Cydney Nielsen +14
Advances in spatial omics and high-resolution imaging enable the creation of three-dimensional (3D) tissue maps that capture cellular organization and interactions in situ. While t…
EasyVitessce: auto-magically adding interactivity to Scverse single-cell and spatial biology plots
Selena Luo, Mark S. Keller, Tabassum Kakar +2
EasyVitessce is a Python package that turns existing static Scanpy and SpatialData plots into interactive visualizations by virtue of adding a single line of Python code. The packa…
Interactive visualization of kidney micro-compartmental segmentations and associated pathomics on whole slide images
Mark S. Keller, Nicholas Lucarelli, Yijiang Chen +13
Application of machine learning techniques enables segmentation of functional tissue units in histology whole-slide images (WSIs). We built a pipeline to apply previously validated…
Safire: Similarity Framework for Visualization Retrieval
Huyen N. Nguyen, Nils Gehlenborg
Effective visualization retrieval necessitates a clear definition of similarity. Despite the growing body of work in specialized visualization retrieval systems, a systematic appro…
scellop: A Scalable Redesign of Cell Population Plots for Single-Cell Data
Thomas C. Smits, Nikolay Akhmetov, Tiffany S. Liaw +3
Summary: Cell population plots are visualizations showing cell population distributions in biological samples with single-cell data, traditionally shown with stacked bar charts. He…
GQVis: A Dataset of Genomics Data Questions and Visualizations for Generative AI
Skylar Sargent Walters, Arthea Valderrama, Thomas C. Smits +5
Data visualization is a fundamental tool in genomics research, enabling the exploration, interpretation, and communication of complex genomic features. While machine learning model…
A Generative AI System for Biomedical Data Discovery with Grammar-Based Visualizations
Devin Lange, Shanghua Gao, Pengwei Sui +4
We explore the potential for combining generative AI with grammar-based visualizations for biomedical data discovery. In our prototype, we use a multi-agent system to generate visu…
Characterizing Multimodal Interaction in Visualization Authoring Tools
Astrid van den Brandt, Sehi L'Yi, Huyen N. Nguyen +2
Multimodal interaction has been increasingly considered in designing visualization authoring tools. However, multimodal interaction has a broad meaning in visualization authoring,…
YAC: Bridging Natural Language and Interactive Visual Exploration with Generative AI for Biomedical Data Discovery
Devin Lange, Shanghua Gao, Pengwei Sui +7
Incorporating natural language input has the potential to improve the capabilities of biomedical data discovery interfaces. However, user interface elements and visualizations are…
Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks
David Kouřil, Trevor Manz, Tereza Clarence +1
Summary: Uchimata is a toolkit for visualization of 3D structures of genomes. It consists of two packages: a Javascript library facilitating the rendering of 3D models of genomes,…