Our mapping method evolved over the course of our earlier work (Johnson and Leon, 1996; Johnson et al., 1998), but has remained consistent since 1999 (Johnson et al., 1999). All maps on this website were produced by the same method, except that recently we have developed software that has accelerated the procedure considerably. The mapping software is available for download on this site, but it currently is specialized for recording average film densities relative to standards in defined olfactory bulb layers of young rats. (Click the following links for either a Users Guide or an Illustrated Description of our mapping software.)  

The mapping software automatically overlays semitransparent images of cresyl violet-stained sections over autoradiographic images of adjacent sections, and it provides tools for section alignment and for adjusting transparency. We use the image of the stained section to locate the glomerular layer and a computer mouse is used to trace a single line between the inner and outer boundaries of the glomerular layer all the way around the bulb. Then, we use the computer mouse to indicate the slope of the midline between the left and right olfactory bulbs. Upon drawing the midline, sampling circles are automatically placed at the intersection of the traced glomerular layer and gridlines chosen to equalize the spacing between adjacent measurements around a section (Johnson et al., 1999). Different grids are stored and used by the software for sections at different relative locations between rostral-caudal landmarks (detected in the cresyl violet-stained sections) to accommodate changes in bulb size and shape along the rostral-caudal extent of the bulbs. The landmarks are the first external plexiform layer, first accessory olfactory bulb, last medial mitral cell layer.  

Overview of the mapping method. By using grids chosen for different relative anterior-posterior positions through the bulb, we generate anatomically standardized matrices that can be statistically analyzed or viewed in various formats included on this website.

The sampling circles have a diameter corresponding to 20µm in the original tissue. There are tools allowing one to reposition or inactivate the sampling circles easily in the event of section tears or folds. One also can skip entire sections in the infrequent event of an entire autoradiographic section being judged to be unmappable. The software writes data files for each section individually as comma-delimited text.  

Screenshot taken while using our mapping software. The circles represent sampling tools positioned at the intersections of stored gridlines and a glomerular layer traced from the overlaid image of a cresyl violet-stained section. The solid red circles have been deactivated by the mapper because they fell off the autoradiography section along a dorsal tear. The hollow red circle is being repositioned. The red wedge represents the constraints imposed by the software during repositioning, and the yellow line is the traced midline between the left and right bulbs, which is used to determine the slope of the gridlines.

For sections anterior to the first accessory bulb, the grids are centered relative to the traced glomerular layer, and the slope of the vertical gridline is determined from the drawing of the midline between the left and right bulbs. For more posterior sections, the grids are centered relative to the subependymal zone, which is traced after the midline is drawn. We map both bulbs of each animal, one side at a time, in this manner. The software also provides tools for analyzing 14C-standards and for determining 2-DG uptake within the subependymal zone at standardized rostral-caudal positions within the bulb. The same software provides tools for data transformation and study-level analysis.