Figure 1.
Positioning probe for acquisition.
The two boxes highlight same field for the two images. A) 2× magnification of swarm plate without probe. Fruiting bodies appear as dark black circles and ovals with bright perimeters. B) White arrow points to probe head positioned over mounds.
Figure 2.
Initial conditions of 2D simulations.
All cells are position randomly throughout domain, but cells that fall within the region of the discs have the orientation set tangent to the radius of the disc. Orientation of cells outside disc is random.
Figure 3.
Bright-field transmitted vs infrared transmitted microscopy.
The two different modes are shown using two different focal planes. A) and C) are focused near the top of the mound, while B) and D) are focused closer to the surface. The large scale irregularities seen in the OCT scans can be optical observed in C) and D). No internal structure is seen in visual light, panels A) and B).
Figure 4.
A single slice of an OCT scan for different scan media.
The dark region is the space above the surface of the agar plate. The red area is the agar. The yellow area is the mound as well as the bacteria on the surface. A) Dry Scan. B) Oil Immersion Scan of mound in (A). C) Dry Scan. D) Glycerol Immersed Scan of mound in (C). Brighter regions below mounds in (A) and (C) demonstrate lensing effects for dry scans.
Figure 5.
3D rendering of fruiting body density.
The top image is a sample mound illustrating a 3D rendering of OCT scan of a mound. The colorbar indicates the intensity value. Higher intensity values corresponds to more back scattered signal which is indicative of regions with higher optical density. In the bottom row, 3D renderings of isovolumes for different intensity values. The intensity value for each isovolume is marked on colorbar. (Lighting and rendering effects causes the color to appear slightly different than the corresponding color in the colorbar).
Figure 6.
Detailed analysis of OCT scan.
Left Column Panel: A 2D rendered cross section from sequence of OCT slices. A) Raw data cross section. B) Gray-Scale image used for image analysis. The elliptical domains for radial density are overlayed on the image. C) Zoomed in region of (B). D) Analysis shows the average intensity (black line) and intensity distribution for cross-sectional discs as a function of height from the base of the mound. The x-axis is the height of each disc in the mound where zero is the base. Data is from mound shown in figure 5. The left plot is the unnormalized data that shows how many pixels have a given intensity value. Middle plot shows the distribution within each disc normalized by the area (total pixels) of each disc. Right plot shows the results from smoothing the distribution of each disc. The black rectangle in all three plots corresponds to the distribution for the cross-sectional disc in (A). E) Analysis showing radial density for four of the elliptical discs at different heights within the mound. Data is from the fruiting body shown in figure 5. The line is from cross-section shown in (B).
Figure 7.
Renderings and shape characteristics of three mounds.
The upper row of images shows 3D renderings of three different mounds. For each mound, the lower row of the figure plots semi-major and semi-minor axis for cross sections as a function of the height from the base of the mound. The orientation as a function of height is shown in same plot. The axis plots are in microns while the orientation is in degrees.
Figure 8.
Angular distribution of intensity averages for experimental cross section.
A) Image of cross section. The white line shows where the reduced intensity occurs around 90 degrees. B) Intensity distribution as a 2D plot. C) Distribution shown as polar plot.
Figure 9.
Simulation results for 1D cells in track model.
A) Plot shows the effect of decreasing the passing probability from 1.0 to 0.1 by looking at the fraction of empty positions in the track. The different curves correspond to different rates of C-signal transfer between neighbors. Results are shown for 20 different values of passing probability and five different transfer rates. Averages were taken from 100 simulations for each set of parameters. B) Spore distribution along circular track for three simulation results. The radial distance corresponds to the number of spores while the angular position denotes the position in the circular track (The outer circle is for a spore count of 10 while the middle circle corresponds to five spores). The passing probability P varies for the three simulations from 1.0 to 0.05. Figure demonstrates how spores clustering is increased as passing probability decreases.
Figure 10.
A–C) Snapshots from simulation over time. Frame (A) shows the initial locations of the first few spores within the mound. Blue arrows in (B) point to regions where groups of two and three spores form together. (C) Later stage of simulation shows the distribution of spores filling in around the disc. D) Spore positions in disc at end of simulation. Radius of disc is 50 microns. E) Local density field for simulation results in (D). Circles show several radii values for radial local density. F) Radial local density distribution for (E).
Figure 11.
Angular distribution of spores for simulated disc.
A) Local density map for 2D simulation. The dashed white line shows where the reduced spore concentration occurs next to high concentration pocket around 150 degrees. B) Concentration of spores in sector of disc as a 2D plot. C) Concentration shown as polar plot.