Visualizing Cells and their Connectivity Graphs for CompuCell3D

Paper
Randy Heiland, Maciek Swat, James Sluka, Benjamin Zaitlen, Abbas Shirinifard, Gilberto Thomas, Andrew Lumsdaine, James Glazier
Developing models that simulate the behavior of different types of interacting biological cells can be a very time consuming and error prone task. CompuCell3D is an open source application that addresses this challenge. It provides interactive and customizable visualizations that help a user detect when a model is producing the desired behavior and when it is failing. It also allows for high quality image generation for publications and presentations. CompuCell3D uses the Python programming language which allows for easy extensions. Examples are provided for performing graph analyses of cell connectivity.

BioVis 2012 Papers & Posters

The New UCSC Cancer Genomics BrowserenRoute: Dynamic Path Extraction from Biological Pathway Maps for In-Depth Experimental Data AnalysisMaTSE: The Microarray Time-Series ExplorerEpithelial Cell Reconstruction and Visualization of the Developing Drosophila Wing Imaginal DiscINCIDE the Brain of a Bee: Visualising Honeybee Brain Activity in Real Time by Semantic SegmentationADVISe: Visualizing the dynamics of enzyme annotations in UniProt/SwissProtGene-RiViT: A visualization tool for comparative analysis of gene neighborhoods in prokaryotesImplicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular SimulationsTowards real-time visualization of detailed neural tissue models: view frustum culling for parallel renderingVisualizing Cells and their Connectivity Graphs for CompuCell3DUncertainty-Aware Visual Analysis of Biochemical Reaction NetworksInteractive Extraction of Neural Structures with User-Guided Morphological DiffusionmzRepeat: Visual Analysis of Lipids in Mass SpectrometryDynamic Channels in Biomolecular Systems: Path Analysis and VisualizationHeterogeneity-based Guidance for Exploring Multiscale Data in Systems BiologySimilarity Analysis of Cell Movements in Video MicroscopyVisualization of Serial Electron Microscopy Images Using Local VarianceVisualization and Exploration of 3D Toponome DataTractography in Context: Multimodal Visualization of Probabilistic Tractograms in Anatomical ContextUsing a Mathematical Graph Framework for Visualization of Inheritance Patterns in Commercial Plant PedigreesExtending The Grammar of Graphics for Biological Data VisualizationcompreheNGSive: A Tool for Exploring Next-Gen Sequencing VariantsMedSavant: Visual Analytics for Genetic Variation DatasetsBulk Synchronous VisualizationGetting Into Visualization of Large Biological Data SetsAracari: exploration of eQTL data through visualizationAn Abstract View of Associations Between Diseases and Developmental Gene SetsCan Adjacency Matrices help in the exploration and understanding of Multi-Omics Data?StratomeX: Enabling Visualization-Driven Cancer Subtype AnalysisGenomeRing: alignment visualization based on SuperGenome coordinatesScalable Interactive Analysis of Retinal Astrocyte NetworksVisual Analysis of Genome-wide Tracts of HomozygosityUser-guided Segmentation of Thoracic Computed Tomography Data for Electrical Impedance Tomography Image Reconstruction