Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.
Modern problem solving environments such as SCIRun have provided scientists with the essential tools for composing complex simulations and visualizations of large scale data. The dataflow programming paradigm has made what was once a rather daunting programming endeavor into a relatively simple point and click process. By condensing the programs into nice little modules that could be visually strung together with pipes, scientists no longer had to worry about the computer programming under the hood. As the new paradigm opened the door to new possibilities and allowed them to explore higher levels of complexity and larger datasets, however, the dataflow networks themselves became rather large and complicated. Scientists now require even greater levels flexibility and organization in dataflow management. For example, it is often necessary for them to construct multiple simulation-visualization scenarios to compare the possibilities and develop new insights.

vistrails vis-spreadsheet1

Figure 1: The VisTrails Visualization Spreadsheet. Surface salinity variation at the mouth of the Columbia River over the period of a day. The green regions represent the fresh-water discharge of the river into the ocean. A single vistrail specification is used to construct this ensemble. Each cell corresponds to a single visualization pipeline specification executed with a different timestamp value.

Developers at SCI are currently working on the next transformation in dataflow management called "VisTrails". VisTrails is a new system that enables interactive multiple-view visualizations by simplifying the creation and maintenance of visualization pipelines, and by optimizing their execution. It provides a general infrastructure that can be combined with existing visualization systems and libraries.

vistrails hist-interface

Figure 2: The VisTrails History Management Interface. Each node in the vistrail history tree represents a dataflow version. An edge between a parent and child nodes represents to a set of actions applied to the parent to obtain the dataflow for the child node.

A "vistrail" (Fig. 2) is an evolving workflow that provides full provenance of the exploration process. A vistrail captures the evolution of a workflow - all the trial-and-error steps followed to construct a set of data products. A vistrail consists of a collection of workflows-several versions of a workflow and its instances. It allows scientists to explore visualizations by returning to and modifying previous versions of a workflow. Instead of storing a set of related workflows, it stores the operations (actions) that are applied to the workflows. A vistrail is essentially a tree in which each node corresponds to a version of a workflow, and the lines between the parent nodes and their children represent the actions applied to parent nodes to obtain the child nodes.

Powerful operations are enabled through direct manipulation of the version tree. These operations combined with an intuitive interface for comparing the results of different work-flows, greatly simplify the scientific discovery process. These include the ability to re-use workflows and workflow fragments through a macro facility; to explore a multi-dimensional slice of the parameter space of a workflow and generate a large number of data products through bulk-updates (see Fig 4); to analyze (and visualize) the differences between two workflows (see Fig 3); and to support collaborative data exploration in a distributed and disconnected fashion.

By maintaining the provenance of both the visualization processes and data they manipulate, VisTrails makes it possible to reproduce dataflow networks at any stage in their development and simplifies the problem of creating and maintaining visualization products. This allows scientists to efficiently and effectively explore data through visualization: they can explore their visualization product by returning to previous versions of a dataflow (or visualization pipeline), apply a dataflow instance to different data, explore the parameter space of the dataflow, query the visualization history, and comparatively visualize different results. Unlike existing dataflow-based systems, in VisTrails there is a clear separation between the specification of a pipeline and its execution instances. This separation enables powerful scripting capabilities and provides a scalable mechanism for generating a large number of visualizations.

vistrails diff-interface

Figure 3:
The Visual Diff Interface.

To better understand the exploratory process, users often need to compare different workflows. The Visual Diff Interface (Fig. 3) allows users to see the differences between the sequences of actions applied to two nodes in the vistrail tree.

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Figure 4: VisTrails Spreadsheet showing the results of multiple visualizations of diffusion tensor data. The horizontal rows explore different color mapping schemes, while the vertical columns use different isosurfaces.

vistrails flow-diag Figure 5

Users create and edit dataflows using the Vistrail Builder user interface. The dataflow specifications are saved in the Vistrail Repository. Users may also interact with saved dataflows by invoking them through the Vistrail Server (e.g., through a Web based interface) or by importing them into the Visualization Spreadsheet. Each cell in the spreadsheet represents a view that corresponds to a dataflow instance; users can modify the parameters of a dataflow as well as synchronize parameters across different cells. Dataflow execution is controlled by the Vistrail Cache Manager, which keeps track of operations that are invoked and their respective parameters. Only new combinations of operations and parameters are requested from the Vistrail Player, which executes the operations by invoking the appropriate functions from the Visualization and Script APIs. The Player also interacts with the Optimizer module, which analyzes and optimizes the dataflow specifications. A log of the vistrail execution is kept in the Vistrail Log.

VisTrails is a new visualization management system that provides the necessary infrastructure to streamline the process of data exploration through visualization. The beta version of VisTrails (including the GUIs) runs on multiple platforms. It has been tested on Linux, Mac and Windows. The current version is being deployed in a select number of collaborator sites. Over the next year, we intend to start a beta testing program in preparation for a future public release.

vistrails logo Download VisTrails!
VisTrails is now available for download and testing. Downloads and documentation are available on the VisTrails Wiki. Plase give it a try and let us know what you think.

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