The Data Visualization and Analysis Environment - DAVE

DAVE [Lifshitz, L. M., Collins, J. A., Moore, E. D. W. & Gauch, J., "Computer vision and graphics in fluorescence microscopy". IEEE Workshop on Biomedical Image Analysis, Seattle, 1994. pp. 166-175. doi:10.1109/BIA.1994.315854] is a large, well-integrated, interactive software system designed especially for displaying and analyzing multi-wavelength, 3-D time series images. It simultaneously displays up to three images acquired using different wavelength fluorescent probes (or perhaps three different time points at a single wavelength), showing individual images in red, green and blue. The images can be displayed as 2-D slices or full 3-D volumes using several different methods for volume rendering, and 3-D volumes can be viewed in stereo using the CrystalEyes viewing system. The images can be interactively rotated and clipped spatially to expose occluded features. Volume data can be simultaneously displayed with polygonal data (e.g. surfaces) or polyline data (e.g., paths). Time series images can be interactively reviewed in real-time, with selected key frames (time points) held on screen as a visual reference. This speed is achieved because DAVE can store all time points as precomputed texture maps and then render them at interactive rates. The co-localization of multiple images can be visually inspected and discretely distributed sites automatically located, sized, and sorted by total fluorescence intensity [Moore, E. D. W. et al. Coupling of the Na+/Ca2+exchanger, Na+/K+ pump and sarcoplasmic reticulum in smooth muscle. , Published online: 14 October 1993; | doi:10.1038/365657a0 365, 657- 660 (1993)]. Dynamics of molecular translocation, activation and concentration change can be evaluated using the same co-localization analysis techniques. Using the DAVE program, the colocalization sites of any two labels can be automatically located, counted, and highlighted, with colocalized voxels prominently displayed (e.g. in opaque blue). DAVE can be used to calculate percent overlap of images, and the probability that such overlap in distribution could have occurred randomly. A somewhat outdated version of DAVE's help pages is online, as are some representative images and movies .

Some of the features of DAVE which are not common among most visualization programs

DAVE allows cursor positioning (for picking objects, voxels, regions or paths) via either a mouse or a MicroScribe-3D input device (a 6 degree of freedom device used in conjunction with two foot pedals which act as a clutch). The cursor can be used in "intelligent" mode, automatically snapping to the brightest nearby voxel when the cursur is clicked. A "snoops" window can be opened in addition to the main window, allowing a zoomed in view of the 3D region surrounding the cursor. This region can be in any of DAVE's display modes (e.g. cubes, see just below). When the cursor is In "tracking" mode DAVE will automatically link up a bright object near the cursor to the nearest bright object in subsequent time points.

DAVE can switch display modes to one which renders each voxel as an individual cube, this aids image exploration and analysis when the values of individual voxels is desired, or visualization of the exact relationship between neighbors pixels.

DAVE's display can be captured and exported as single images, or a movie can be made of any sequence of actions taken within DAVE. After spending time adjusting DAVE's display parameters, viewing angle, zoom factor, etc, all those settings can be easily saved as a named "slide". All slides produced during a session can be saved as a text "slideshow" file. This file can be read back in at any time; the user can then easily switch between different views by simply clicking on the name a slide. This restores the previously saved viewing parameters, leaving the user in a "live" view so that the image can be manipulated just as before (ie, a slide is not a stored static 2D image).

DAVE can synchronize with another version of DAVE running remotely. Thus if researchers at two sites load the same dataset, the researcher a one site can setup a desirable view of the data and then have the remote DAVE display that exact view. DAVE can also synchronize with other locally running programs - if they are written to communicate using DAVE's protocol. This permits, for instance, a locally running deformable model to send its surface to DAVE to be dynamically shown during its deformation process; similarly the deformable parameters can then be changed within DAVE and sent back to the deformable model program, modifying its behaviour.

All of the features available in this system are too numerous to detail, arising from more than 100,000 lines of C code. A somewhat outdated version of DAVE's help pages is online, as are some representative images .