This thesis describes methods and first analyses to study the shape and motion of a large school of approximately 2000 Harengula clupeola (false herring) in three-dimensional space. This school of fish was present at the large-scale and publicly accessible ocean aquarium of the Rotterdam zoo, in the Netherlands known as Diergaarde Blijdorp, from spring 2017 to summer 2020.@en

The circular Taylor-Couette flow is one of the archetypical model systems for the study of flow transitions and dynamic pattern formation in experimental fluid dynamics. The emergence of the internal vortical flow structures are commonly visualized through a rheoscopic flow visualization, while their spatio-temporal dynamics can be extracted by the construction of a space-time diagram using a single camera. Although the latter is an effective method to map the various flow regimes for different inner and outer cylinder rotations, it suffers from limitations in the frame rate while the full extent of the azimuthal vortex structure along the circumference, together with its dynamic evolution through space and time, remains unclear. In this work, we perform the full 360-degree field of view panorama imaging for the rheoscopic flow visualization of the azimuthal vortex structure that wraps around the circumference. We use a set of 12 GoPro cameras that are commercially available and can be triggered remotely. We calibrate and position our cameras using methods from computer vision while we synchronize their audio channels at an inter-frame precision much greater than the frame rate. We unwrap the physical coordinates along the circumference of the outer cylinder through texture mapping its surface using a spatially weighted image interpolation and present a single representation of the azimuthal vortex structure from the rheoscopic flow visualization. We validate our methods within a submillimeter precision and showcase the application to study the steady-state and transient dynamics of a single- phase wavy vortex flow. Furthermore, we discuss the current limitations as we add neutrally buoyant PMMA particles at increasing volume fractions up to 30 %. Our methods allow us to fully decouple space and time, and study the dynamic pattern formation at bullet time accuracy. @en

The accumulation of motile cells at solid interfaces increases the rate of surface encounters and the likelihood of surface attachment, leading to surface colonization and biofilm formation. The cell density distribution in the vicinity of a physical boundary is influenced by the interactions between the microswimmers and their physical environment, including hydrodynamic and steric interactions, as well as by stochastic effects. Disentangling the contributions of these effects remains an experimental challenge. Here, we use a custom-made four-camera view microscope to track a population of motile puller-type Chlamydomonas reinhardtii in a relatively unconstrained three-dimensional (3D) domain. Our experiments yield an extensive sample of 3D trajectories including cell-surface encounters with a planar wall, from which we extract a full description of the dynamics and the stochasticity of swimming cells. We use this large data sample and combine it with Monte Carlo simulations to determine the link between the dynamics at the single-cell level and the cell density. Our experiments demonstrate that the near-wall scattering is bimodal, corresponding to steric and hydrodynamic effects. We find, however, that this near-wall dynamics has little influence on the cell accumulation at the surface. On the other hand, we present evidence of a cell-induced surface-directed rotation leading to a vertical orbiting behavior and hopping trajectories, consistent with long-range hydrodynamic effects. We identify this long-range effect to be at the origin of the significant surface accumulation of cells.

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Abstract: Obtaining accurate experimental data from Lagrangian tracking and tomographic velocimetry requires an accurate camera calibration consistent over multiple views. Established calibration procedures are often challenging to implement when the length scale of the measurement volume exceeds that of a typical laboratory experiment. Here, we combine tools developed in computer vision and non-linear camera mappings used in experimental fluid mechanics, to successfully calibrate a four-camera setup that is imaging inside a large tank of dimensions ∼10×25×6m3. The calibration procedure uses a planar checkerboard that is arbitrarily positioned at unknown locations and orientations. The method can be applied to any number of cameras. The parameters of the calibration yields direct estimates of the positions and orientations of the four cameras as well as the focal lengths of the lenses. These parameters are used to assess the quality of the calibration. The calibration allows us to perform accurate and consistent linear ray-tracing, which we use to triangulate and track fish inside the large tank. An open-source implementation of the calibration in Matlab is available. Graphic abstract: [Figure not available: see fulltext.].

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Obtaining accurate experimental data from Lagrangian tracking and tomographic velocimetry requires an accurate and consistent camera calibration over multiple views. At length-scales that span beyond the laboratory environment obtaining a camera calibration can be challenging. Combining tools developed in computer vision and non-linear camera mappings known from experimental fluid mechanics, we successfully calibrate a four-camera setup at the large-scale ocean aquarium of the Rotterdam Zoo. The method is valid for any number of cameras and allows retrieving the intrinsic and extrinsic camera properties that can be used to compute the (virtual-)camera positioning and further quality assessment. Using our method we obtain an accurate and consistent camera calibration at largescale over a space that has limited access. @en

Mixing and spreading of different liquids are omnipresent in nature, life and technology, such as oil pollution on the sea, estuaries, food processing, cosmetic and beverage industries, lab-on-a-chip devices, and polymer processing. However, the mixing and spreading mechanisms for miscible liquids remain poorly characterized. Here, we show that a fully soluble liquid drop deposited on a liquid surface remains as a static lens without immediately spreading and mixing, and simultaneously a Marangoni-driven convective flow is generated, which are counterintuitive results when two liquids have different surface tensions. To understand the dynamics, we develop a theoretical model to predict the finite spreading time and length scales, the Marangoni-driven convection flow speed, and the finite timescale to establish the quasi-steady state for the Marangoni flow. The fundamental understanding of this solutal Marangoni flow may enable driving bulk flows and constructing an effective drug delivery and surface cleaning approach without causing surface contamination by immiscible chemical species.

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