Data Analysis and Visualization Environment - movies and static images

DAVE's User Interface

An image (to the left) and a 17 MB mpg movie showing DAVE's user interface and rendering window. The data shown is a dual labeled smooth muscle cell. The green label is bound to the BK (big conductance potassium) channels on the plasma membrane. The red label is bound to Ryranodine receptors inside the cell; this is the release site for Calcium ions which then diffuse to the BK channels to help activate them. It is therefore important to locate the Ryranodine receptors and BK channels and determine the distance from each Ryanodine receptor to the nearest BK channels (closer BK channels will be more likely to activate since they see higher Calcium levels). The boxes shown in the video are the automatic determination of those sites and the blue lines connect the Ryanodine receptors to the nearest BK channels. DAVE can switch between many rendering modes, some of which are lower resolution (to permit quick interaction) which others are full resolution. The lower resolution modes are no longer used very much since graphics hardware has gotten much faster. Data acquired with Ronghua ZhuGe. DAVE has tens of control windows each with a different function. Only those needed for the video are shown.
reference: Spatial organization of RYRs and BK channels underlying the activation of STOCs by Ca(2+) sparks in airway myocytes. Lifshitz LM, Carmichael JD, Lai FA, Sorrentino V, Bellvé K, Fogarty KE, ZhuGe R. The Journal of general physiology. 2011; 138(2):195-209.

Opaque and Semi-transparent surfaces (via the Marching Cubes algorithm with DAVE) of Pericentrium Images

This is a dual-labeled pericentrium image. Data acquired with Stephen Doxsey. To see a quicktime movie of the image click here (approx 6.5 Megabytes).

This is a dual-labeled pericentrium image with a marching cubes surface. Data acquired with Stephen Doxsey. To see a quicktime movie of the image click here (approx 18.5 Megabytes).

Volume Data, Surfaces, and Arbitrary Cross-sectional Planes in Dual-labeled Neurons

A rat neuron was labeled for Vasopressin (green) and Serotonin (red) and rendered several different ways. The middle image is a two color volume rendering. The left image shows two planar slices of the Vasopressin image (in grayscale, one slice cutting obliquely through the data set). The plasma membrane of the neuron is shown as a yellow wire mesh. Volume data is not displayed. The right image is similar to the left image except the plasma membrane is shown as a surface and the volume data is displayed. Data acquired with Craig Ferris.

Volume data displayed a cubes, the nuclear membrane as a surface

This shows labeled mRNA within a cell. The red/gray surface is part of the nuclear envelope (red = inside, gray = outside), which was manually outlined (DAVE then automatically stretches a surface over the wireframe). mRNA was labeled and voxels with label are displayed as shaded cubes (color relates to the intensity of the voxel). Sites with large clusters of mRNA just inside the nuclear envelop are probably transcription sites. This data (although not this exact image) was used for the cover of Science vol 240, April 24, 1998. A slightly different view is shown to the right. Data acquired with Andrea Femino.

Time mapped to the third dimension, volume data (calcium concentration) mapped to surface color

To study the effects of Calcium concentration on the direction of cell movement we labeled a Eosinophil with a calcium sensitive indicator and imaged it as it moved over time, producing a 2D time series. The left rendering shows images from the time series, with time being the third dimension. The labeled cells are in slightly transparent gray (black = low calcium, which = hi calcium). Their center axis is shown as a color scale (blue = low calcium, red/white = high calcium). Two pseudopodia (green surfaces) and the leading lamellipod (yellow) are shown. A slightly different view is shown to the right. It now no longer shows each separate time point (2D gray surface) but rather draws a translucent surface over the entire time series. Similarly the central axis is now connected through time so it appears as a sheet. Data acquired with Susan Gilbert.

Tripled labeled volume data

Tripled labeled neurons are rendered as a 3D volume (top left image), red = Tyrosine hydroxylase vesicles, green = neurotensin receptors, blue = retrograde tracer. The background color can also be changed (top right image), obscuring the dim label. By only displaying a subvolume (bottom left image) the interior of structures is easier to see. Data acquired with Craig Ferris.

Opaque and semi-transparent surfaces along with volume data

Images of a deforming surface moving toward Vinculin (green) on the plasma membrane of smooth muscle cell. The initial starting surface (top left image) is shown as an opaque surface. As the surface deforms (going right to left, top to bottom) it is turned partly transparent. The surface continues to deform, finally resulting in a fit to the plasma membrane (2nd to last image). The final surface can also be viewed as an opaque surface (bottom right image). Data acquired with Ed Moore.