Davis: Data Viewing System

Abstract

Davis (Data Viewing System) is a general-purpose data viewer designed for the simultaneous display of a large number of dynamic data sets. Davis was inspired by the need to explore computational models of the cerebral cortex. These systems are distinguished by complex dynamic elements interconnected in irregular patterns. Neuroscientists study the detailed behavior of individual elements and how these elements interact to achieve cortical function. This paper describes Davis and its use in cortical visualization.

Davis is written in Java and can be run from a browser or as a standalone application. Users must provide an XML description of their data, which Davis uses for its menus, browsing and visualization. Davis visualizations can be applied to any collection of space-time data sets, and the Davis infrastructure allows visualizations to be added easily.

Davis Beta

Davis is now available for beta testing. See Download instructions.

Participants

Kay Robbins (faculty)
Cory Burkhardt (staff software developer)
Egle Pilipavicuite (graduate student)
Dragana Veljkovic (graduate student)
Jason Edwards (undergraduate)
James Packer (undergraduate)

Alumni

Kevin Allen (undergraduate)
Robert Baltimore (graduate)
Igor Grinshpan (graduate)
Zheng Zhi (graduate)

Current Sponsors:

NSF/NIH Collaborative Research in Neuroscience (NSF EIA-0217884): Web
NIH (G12 RR13646)

Previous Sponsors:

NSF ACI-9721348 Web
ONR N00014-97-0029 Web

Davis views

This figure shows sample views from Davis. The left window displays data from a simulation run of the Nenadic/Ghosh/Ulinski (NGU) model of the turtle visual cortex containing approximately 1000 neurons. The display represents each neuron by a shape, with different types of neurons displayed by different shapes. The magnitude of the response is represented by color with red indicating greater intensity. The shape, size, and color mapping are user-settable in this visualization,

Since Davis is intended to be used with many simultaneous windows, several optimizations are applied to the views. For example, this view keeps track of the previous color of each element and does not redraw a pixel unless it is in the foreground and the color changes. The visualization also uses a settable quantization to reduce the number of possible colors and therefore also the number of pixels that are redrawn on each frame. These simple optimizations reduce the computational load by a factor of 10 or more for some of the neural data tested with Davis. The display uses tool tips to identify individual elements and their current values as the user moves the cursor over the figure.

If the user double clicks on a neuron in the main Davis view, a plot of the response for an individual neuron appears. The red radio line in this single neuron plot advances across the display to mark the current time.

Davis uses a VCR metaphor for control. The upper row of three buttons presents a standard VCR control (Play, Pause, Stop). The left widget in the middle row controls the display rate. Delay regulates the display time between successive frames, with larger delay values corresponding to slower display rates. The widgets of the bottom row allow manual navigation through time. By dragging the slider with the mouse, the user can manually step through the frames. The right and left single arrow buttons allow the user to single step through the frames at the specified sampling rate. The double arrows move the time to the beginning or to the end.

Comparing behavior of multiple variables

The four windows display soma voltage and their KL decompositions for different types of neurons in the NGU model. The upper left window displays the same data as the main Davis viewing window shown above. Five different types of neurons (lateral, medial, stellate, horizontal and LGN) are displayed with different shapes.

The three KL phase portraits shown in this graphic give low-dimensional caricatures that reveal the structure and timing of the response for different types of neurons. The red dot in each KL window specifies the position of the current frame in the caricature. In each picture, the origin corresponds to t = 0, since the first frame was subtracted from all of the other frames before doing the KL decomposition. The current frame may be interpolated if the timer is not running at a rate commensurate with the sampling frequency of the measurement group. The upper right KL window depicts the soma voltage for the lateral neurons, the lower left KL window depicts the soma voltage for medial neurons, and the lower right KL window depicts the soma voltage for the horizontal cells.

The lateral and medial cells have an initially linear expanding wave of response. The first bend in the curve is reached when the first response wave reaches the left edge of the brain. The upper branches of the lateral and medial KL caricatures represent the post-stimulus decay of the response. The data set spans 1.5 seconds. The KL curves do not return to 0 because the lateral and medial neurons are still hyperpolarized 1.5 seconds into the response. The KL decomposition of the inhibitory horizontal cells (lower right KL window of the left grouping) reveals that these neurons have not exerted any significant inhibitory restraint at this point in the response. The inhibitory stellate neurons (whose KL decomposition is not shown here) activate much earlier in the response and have a smooth caricature, suggesting that stellate cells play a different, more coherent inhibitory role.

Using Davis to study effect of AMPA

An important question is the effect of physiological parameters on the model's behavior. For example, the amount of excitation generated by AMPA conductance depends on the strength of synaptic coupling constants which must be chosen by the modeler. The figure shows how the response changes when the AMPA coupling constants are changed. The top row shows the response when the AMPA coupling is 4 times stronger than that shown above, and the lower row shows the response when the AMPA coupling is halved. The response is shown at 97 ms as in the previous figures.

Notice that at 97 ms, the response for the strengthened AMPA is much more developed than that for a model with the normal AMPA conductances. The KL decomposition does not show the linear growth followed by a sharp change in direction. Also, the response shows no sign of damping, but rather, it oscillates for the full 1.5 seconds encompassed by the run. The response for a system with AMPA coupling that is twice as strong is qualitatively similar to that shown for multiplication by 4. When AMPA is halved, the response is much less vigorous, but the wave does reach the edge of the brain before dying away.

Davis Input

Davis has been designed without hard coding the specifics of any particular data set into the program. The viewer uses an XML specification for the input of the data set relationships. Each environment is represented by an XML file following the schema below. This sample Davis menu allows the user to select data sets to display.

Environments are available through the pull down menu at the top of the selection window. The viewer has selected the NGU model with sorted coordinates (Nenadic-Ghosh-Ulinski Model Sort) as the environment. The environment name is used as a key into a configuration file that holds the file names of the XML files representing the environments. The viewer uses these XML files to build the menu and to input the data. The visualization is based entirely on this XML file rather than on hard-coded information.

Davis XML Schema

Rather than using hardwired visualizations for particular biological problems, Davis uses a problem space model based on the schema for an environment. Each problem space or domain is defined by an environment that has coordinate groups, parameters and experiments. Different numerical models or different experimental setups are organized into distinct environments.

The coordinate group forms an organizational unit of elements that are to be treated in the same way by visualization. Examples of coordinate groups include neurons of a particular type, calcium channels, grid points for interpolated data, photodiodes, or even virtual points that have been placed to obtain a particular visual effect. Each element in a coordinate group has a spatial position and is associated with one or more time series.

A single data set can be partitioned into coordinate groups in many different ways. For example, stellate neurons may be placed in a single coordinate group, specifying that each stellate neuron is to be treated as a unit. Alternatively, data from individual compartments of the stellate neurons can be dumped separately. In this case, each type of compartment in the stellate neurons would form a distinct coordinate group with its own set of positions.

Publications

Synchronized views for exploring populations of neurons
K. A. Robbins, I. Grinshpan, K. Allen and D. M. Senseman (2004)
Proc. SPIE (Papers selected from Visualization and Data Analysis 2004, Eds Robert F. Erbacher, Philip C. Chen, Jonathan C. Roberts, Matti T. Gröhn, Katy Börner), 5295:235-245.

Visualizing cortical waves and timing from data
K. A. Robbins, M. Robinson and D. Senseman (2004)
IEEE Visualization 2004, 401-408.

Using derivatives to compare cortical waves across preparations
K. A. Robbins and D. M. Senseman (2003)
Neurocomputing, 52-54:885-891.

Abstracts and Presentations

Using davis to compare neural models
E. Pilipavicuite, K. A. Robbins and D. M. Senseman
Wam Bamm 2005, San Antonio, TX Mar 31 - Apr 2.

Structure of cortical waves
K. A. Robbins and D. M. Senseman
9th RCMI International Symposium on Health Disparities, Baltimore, MA Dec. 8–12.

Synchronized views for exploring neuronal populations
K. A. Robbins, I. Grinshpan, K. Allen, E. Pilipaviciute and D. M. Senseman
Computational Neuroscience (CNS ‘2004) Baltimore, MD July 18-22, 2004.

Exploring behavior of neuronal populations with Davis
K. A. Robbins I. Grinshpan, K. Allen and D. M. Senseman
Soc. For Neuroscience Abstracts 2003.

Dynamical systems analysis of propagating waves in turtle visual cortex
P. Ulinski, B. Ghosh, K. A. Robbins and D. M. Senseman
2003 SIAM Conf. on Applications of Dynamical Systems (DS03), Snowbird, UT.

Exploring behavior of neuronal populations with Davis
K. A. Robbins I. Grinshpan, K. Allen and D. M. Senseman
2003 RCMI Spring Symp., Abstract 1021, San Antonio, TX.

Visualizing neuronal models for exploration
I. Grinshpan and K. A. Robbins
GUM'2002, San Antonio TX, 2002.