On the Patterns Page, we provide an image of the activity pattern evoked by the odorant under the exposure conditions displayed. A number of different views are offered and can be chosen using the selectors beneath the pattern. Once a view type is selected, all patterns during that session will be viewed using that type unless another type is selected. 

The default view is a color-coded 2-D contour chart wherein warmer colors are used to represent higher uptake. The default orientation is ventral-centered, so that the charts take the form of a rolled-out map of the glomerular layer after a cut is made along the dorsal surface running from anterior to posterior. In our print publications, we prefer the ventral-centered format because it minimizes the impact of missing values along the dorsal aspect of the bulb, where we occasionally lose tissue during sectioning in the cryostat. Many other researchers in the field prefer the dorsal-centered format. This format has the advantage of representing with less distortion the dorsal area of the bulb, which recently has received inordinate attention as a result of the use of optical imaging techniques that most conveniently access this part of the bulb.  

Comparison of the two orientations used for our two-dimensional images of bulbar activity patterns. 

The rendering of a three-dimensional surface in only two dimensions necessitates distortions of the space relative to the original shape. These distortions are minimal in the center of the 2D rendering. To avoid these kinds of distortions, we also provide a rotatable 3D model of the surface of the glomerular layer, which is discussed in greater detail below. 

We offer three different methods for representing activity levels. A pop-up showing the color or gray level scale used with the selected view type can be seen by clicking the button on the top right of the page. The default, color-coded contour charts have a certain advantage in that the colors can be compared readily from pattern to pattern to identify clearly any given activation level. However, a small difference in activity can result in a dramatic transition from one color to another within one part of the scale (e.g., from green to yellow), while a similar difference in activity at another part of the scale (e.g., from blue to green) can appear to be less remarkable. As one way of facilitating the correct interpretation of these color differences, we have included on this website the option of viewing the color-coded contour charts on a surface plot where the z-score values are plotted along a z-axis. In these plots, the relative height of peaks can be used to evaluate the actual difference in z-score values. The third method of representing activity levels is through grayscale bitmaps, wherein the difference in gray level at each step of the scale is proportional to the change in activity levels. Another advantage of this method is that each pixel of the image represents a single value in the underlying database, allowing a more direct illustration of the actual data. Another apparent advantage of the grayscale bitmap charts is that they use more steps to illustrate the range of activity levels in the data matrices, which confers a greater richness of texture to the patterns, allowing one to see potential patterns that lie within any given color range of the contour charts. However, given that the differences between sequential gray levels are so small, many of these details may not be representative of the patterns in individual animals. Another disadvantage of the grayscale maps is that optical illusions involving relative contrast of adjacent gray levels can make it very difficult to compare levels of uptake across different patterns.  

The same activity pattern, evoked by valeric acid, is shown here using three different view types, each of which possesses its own advantages and disadvantages. By presenting these choices, we hope to more truly convey the pattern evoked under each exposure condition. All three versions shown here are ventral-centered. Dorsal-centered versions of the same three types of charts also are available on the site. 

We have developed a surface-based three-dimensional model to display the two-dimensional data matrices of odorant-evoked activity, allowing the viewer to consider the responses evoked by odorants in the more familiar form of an olfactory bulb. This approach permits the data matrices to be viewed from any perspective and compared to other data matrices on our website. It also avoids many of the distortions that are introduced by flattening a three-dimensional surface into two dimensions. 

Shown here is a pattern of 2-DG uptake evoked by valeric acid. On the left is our conventional, 2-dimensional contour chart in a ventral-centered format. On the right is a snapshot of the same pattern appearing as a texture on our rotatable 3D model  

We reconstructed the glomerular layer of a single olfactory bulb by digitizing images of stained coronal sections, drawing the outline of the glomerular layer, and then meshing together the outlines to create a detailed model. A more generic model then was created using a similar approach with fewer sections and simpler geometry to approximate the detailed model, thus decreasing greatly the number of vertices and edges. This generic model is what is being used to display the data matrices of odorant-evoked activity on this website. (Click here to follow links to software needed to use this model.) The source code for this model also can be downloaded from this site.