rotating around a point near the helictoglossa is shown, on the right (b) a sketch of the diatom with raphe.Figure 1.16 Surirella biseriata in valve view.Figure 1.17 Trajectory of a Surirella biseriata. The driving side changes at the reversal points.Figure 1.18 Paths of Surirella biseriata in a culture. They were visualized by overlaying frames of a video.Figure 1.19 Pinnularia viridiformis with a length of approx. 90 μm.Figure 1.20 Places within and on a biofilm where Pinnularia viridiformis can be found. The typical movement patterns are indicated by arrows. Shunting movements are marked with short arrows at both apices.Figure 1.21 Superimposed frames of a video during the standstill of a diatom. A tension has built up in the biofilm.Figure 1.22 Nitzschia sigmoidea on the water surface viewed with PlasDIC.Figure 1.23 Nitzschia sigmoidea with a stereomicroscope in oblique view.Figure 1.24 Sketch of a Nitzschia sigmoidea on the water surface seen from the horizontal direction.Figure 1.25 Sketch of two adjacent Nitzschia sigmoidea on the water surface seen from the horizontal direction.Figure 1.26 Very regular structure of a diatom cluster on the water surface (dark field).Figure 1.27 Relative speed of two diatoms plotted versus their distance.Figure 1.28 Energetically favorable patterns of three diatoms on the water surface: all diatoms parallel (a) and diatoms form a triangle (b).Figure 1.29 Frequently observed movement patterns: movement along the raphe (a) and angular changes at connected apices (b).Figure 1.30 Image sequence showing the temporal development of seven connected diatoms. The time between the first and last image is 170 seconds.Figure 1.31 Pinnularia gentilis.Figure 1.32 Cymbella lanceolata.Figure 1.33 Two small colonies photographed with PlasDIC.Figure 1.34 Elementary steps that contribute to structure formation.Figure 1.35 Movement activity of diatoms between colonies.Figure 1.36 Colonies at the beginning of intensive light irradiation (a) and after about two hours (b).Figure 1.37 Cymbella culture in the light phase (a) and dark phase (b).Figure 1.38 Number of free diatoms (blue) and the number of diatoms bound in colonies (red) over 24 days. A yellow bar indicates the phases of bright light.Figure 1.39 Total number of diatoms (red) with exponential fitting (blue).Figure 1.40 Number of diatoms in motion over the last 10 observation days.
2 Chapter 2Figure 2.1 The polycarbonate channel used to image diatom motion, photographed on the stage of the inverted microscope. The depth, width, and length of the channel are 1 mm, 2 mm and 60 mm, respectively. A glass slide was bound to 2.5 mm × 7.5 mm polycarbonate block using two pieces of double-sided tape placed on the polycarbonate block. The coordinate origin coincides with the origin for the pixels. Diatoms move on the glass slide at the bottom of the chamber. The inset figure shows a schematic diatom, the coordinate axes, and the origin, in the plane of the top of the slide.Figure 2.2 (a-b) Scatter plots of the simulated test object and the stationary polystyrene particle centroids, respectively. The stationary polystyrene particle was imaged at 821 fps. The number of points plotted is 1000 for the simulated particle and 4000 for the polystyrene particle.Figure 2.3 Displacement histogram of the diatoms (symbols) and stationary polystyrene particle (continuous line) imaged at 821 fps.Figure 2.4 (a) Plot of total displacement as a function of time in a diatom centroid measurement. The frames around the arrow are investigated in detail. (b) Overlay image of the diatom boundary for frames where the displacement was 293 nm at 1986 ms. White pixels show the overlapped points in the diatom boundary, while colors indicate change in boundary location; (c) and (d) show two consecutive frames of the diatom (diatom #2) for the displacement shown by an arrow in Figure 2.4 (a). The boundaries were calculated using the “Binary Centroid” algorithm. In b, green = frame c and magenta = frame d.Figure 2.5 Angular velocity histogram of the diatoms #1-3 that were imaged at 821 fps. The diatoms exhibited changes in their orientation angles as they traversed the imaging strip horizontally.Figure 2.6 In Figures 2.6a and 2.6c the orientation angle corresponding to the diatoms whose trajectories were previously investigated are shown (diatoms #2 and #3 in a and c, respectively). In Figure 2.6e the orientation angle of another diatom (diatom #4) is shown. Orientation angle is the angle between the major axis of the diatom and the x-axis. Figures (b), (d), and (f) are overlay images of the diatom boundary for different frames of the data shown in (a), (c), and (e), respectively. White pixels show the stationary points in diatom boundary, while colors indicate change in boundary location. An extra Gaussian smoothing was included in the image processing algorithm for the diatom #4, whose orientation angle is shown in Figure 2.6e. Otherwise, it was not possible to extract orientation data for diatom #4.Figure 2.7 (a) The diatom in Figure 2.6d is rotated around the arc center of the white pixel region in Figure 2.6d; (b) the consecutive intersections of the major axis of the diatoms during rotation are shown as yellow dots. In (b), while the green dots at the centerlines are close to one another, they would coincide exactly if the rotation were precisely around the center of the diatom.Figure A1 Displacement histograms of the image of the stationary polystyrene particle situated in the micromachined channel; (a) and (b) show x and y displacement histograms, respectively. Dots represent microscopy measurement while continuous lines are the Gaussian fits to the measurements. Two Gaussian terms are used for fitting total displacement data. The particle was imaged at 821 fps.Figure A2 Fast Fourier Transform (FFT) of the x and y coordinates of the centroid location for the recordings made with the stationary polystyrene particle and a diatom; (a) and (c) are the FFTs of the x centroid data and (b) and (d) are the FFTs of y centroid data of the polystyrene particle and diatom #3, respectively. Prior to the FFT the centroid location mean was subtracted from the data.Figure A3 Representative trajectories of the centroids of diatoms #1, #2, and #3 are given in (a), (b), and (c), respectively, over 500 frames. The diatoms were imaged at 821 fps.Figure A4 Zoomed in views of the large displacements in the representative trajectories given in Figure A3. The plots (a), (b), and (c) show the centroids of diatoms #1, #2, and #3, respectively.Figure A5 Mean square displacement (MSD) data of diatom trajectories. Diatom motion recordings were divided into segments that are 500 frames long and MSD data of each segment was calculated. The black dashed line represents the mean MSD and red line represents the best fit to the MSD for all diatoms (diatom #1 – (a), diatom #2 – (b), diatom #3 – (c)). All MSD data falls into the range shown by gray shaded areas in the figures.Figure A6 Normalized velocity autocorrelation of all the