Visualization for 3D Visualization for 3D Microscope DataMicroscope Data

Jonathan RobbinsJonathan Robbins

PurposePurpose

• Provide a tool to assist scientists Provide a tool to assist scientists visualize 3-D datavisualize 3-D data

Motivating ProblemsMotivating ProblemsCystic FibrosisCystic Fibrosis

How does the mucus layer interact with the cilia?

Motivating ProblemsMotivating ProblemsWhere do proteins attach to Dendritic Spines?Where do proteins attach to Dendritic Spines?

Motivating ProblemsMotivating ProblemsImaging Kinetochores During MitosisImaging Kinetochores During Mitosis

Current VisualizationCurrent Visualization

• View each slice separatelyView each slice separately• View 3-D visualizations from fixed View 3-D visualizations from fixed

camera positionscamera positions

Our SoftwareOur Software

• Enables user to adjust camera Enables user to adjust camera position arbitrarily and in real-timeposition arbitrarily and in real-time

• User can switch among various User can switch among various visualization techniquesvisualization techniques

• Rendering done by VTKRendering done by VTK• Interface written with Java SwingInterface written with Java Swing

VTKVTK

• Visualization Toolkit developed by Visualization Toolkit developed by Kitware, Inc. Kitware, Inc.

• Open-source 3-D data visualization Open-source 3-D data visualization softwaresoftware

• Written in C++Written in C++• Wrappers in Java, Python, and Tcl.Wrappers in Java, Python, and Tcl.

DemoDemo

Where do we go from Where do we go from here?here?

• Extensions to VTKExtensions to VTK– 12-bit TIFF files12-bit TIFF files– Read file types not currently supported by Read file types not currently supported by

VTKVTK– Support Volume rendering of multipleSupport Volume rendering of multiple– datasetsdatasets

• Improved techniques for selecting Improved techniques for selecting isovalues and transfer functionisovalues and transfer function– Would like to be able to select a feature and Would like to be able to select a feature and

have the isovalue and transfer function have the isovalue and transfer function automatically set to display similar features automatically set to display similar features