Mark S. Keller
6 papers 2024–2026
How Do We Visualize Space in Molecular Biology? A Study of Spatial Transcriptomics Visualization Practices
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 study this by...
Use-Coordination: Model, Grammar, and Library for Implementation of Coordinated Multiple Views
Pluot: Towards 'write once, run everywhere' visualization software
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, an architecture...
EasyVitessce: auto-magically adding interactivity to Scverse single-cell and spatial biology plots
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 package uses Vitessce...
Interactive visualization of kidney micro-compartmental segmentations and associated pathomics on whole slide images
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 segmentation...
scellop: A Scalable Redesign of Cell Population Plots for Single-Cell Data
Summary: Cell population plots are visualizations showing cell population distributions in biological samples with single-cell data, traditionally shown with stacked bar charts. Here, we address...