Extended Data Fig. 1: Overview of the robotic setup that was constructed to automatically extract cells with high spatiotemporal accuracy from the swarm.

(a), Photograph of the assembled robot, positioned on the right-hand side of the microscope objective. The inset photograph shows the robotic arm and sampling tip directly above the objective while it picks up cells from the swarm inside the Petri dish. The long horizontal stage in the central area of the main photograph (stage #1 in panel d) moves the robot back and forth between the sampling tips (bottom right), the petri dish containing the swarm placed on the microscope objective (left, outside of the image field of view, but shown in the inset photograph) and back to the sample ejection area (Eppendorf tubes within a cooled box in the central bottom part of the image, see also panel d for a schematic overview of the whole setup). Protective lids, which are placed on the tip box and sample ejection box were removed for the photograph to better show all components. The inset photograph also shows a transparent acrylic cover on top of the enclosure containing swarm to keep humidity high, with an opening for the sampling tip that is covered by a removable plastic plate (grey plate visible in the inset photograph), operated by a robotic stage (stage 4 in panel d). (b), 3D rendering of the robot, using approximately the same viewing angle as in panel a, with the protective lids on the tip box and sample ejection box removed to better show the components. The 3D rendering files can be downloaded from the Zenodo repository (DOI: 10.5281/zenodo.8229225), in a format that can be viewed in the AutoDesk Inventor software; for convenience, the 3D rendering can be viewed online with full control of the viewing angle: https://gmail3493581.autodesk360.com/g/shares/SHd38bfQT1fb47330c99c60340a060ffa874. (c), Top view of the 3D rendering, showing all components including protective lids. Robotic stages are labelled consistent with numeric labels in panel d. (d), Schematic top view of the robotic setup, including the XY stage of the microscope. The robotic stages #1, #2, #4 refer to an individual stage, while #3 refers to a group of stages described further in panels e and f. (e), Detailed 3D rendering view and photograph of the group of stages labelled #3 in panel d. This group of stages consists of several linear stages (stages 3.1, 3.2, 3.4, 3.5) and one rotational stage (stage 3.3). Attached to stage 3.4 is a tip holder (grey), which mimics the shape of the bottom part of a pipette, such that pipette tips can be picked up. Stage 3.5 mimics the ejection mechanism of a pipette, enabling automatic tip ejection. (f), Schematic side views of the group of stages labelled #3 in panels d and e. How these stages are operated to perform sampling from the swarm is described in the Methods section.