A three-dimensional (3D) scanning velocimetry system is developed to quantify the 3D configurations of particles and their surrounding volumetric, three-component velocity fields. The approach uses a translating laser sheet to rapidly scan through a volume of interest and sequentially illuminate slices of the flow containing both tracers seeded in the fluid and particles comprising the aggregation of interest. These image slices are captured by a single high-speed camera, encoding information about the third spatial dimension within the image time-series. Where previous implementations of scanning systems have been developed for either volumetric flow quantification or 3D object reconstruction, we evaluate the feasibility of accomplishing these tasks concurrently with a single-camera, which can streamline data collection and analysis. The capability of the system was characterized using a study of induced vertical migrations of millimeter-scale brine shrimp (Artemia salina). Identification and reconstruction of individual swimmer bodies and 3D trajectories within the migrating aggregation were achieved up to the maximum number density studied presently, $8 , times,10^5$ animals per $textrm{m}^3$. This number density is comparable to the densities of previous depth-averaged 2D measurements of similar migrations. Corresponding velocity measurements of the flow indicate that the technique is capable of resolving the 3D velocity field in and around the swimming aggregation. At these animal number densities, instances of coherent flow induced by the migrations were observed. The accuracy of these flow measurements was confirmed in separate studies of a free jet at $Re_D = 50$.
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