Gigapixel behavioral and neural activity imaging with a novel multi-camera array microscope

The dynamics of living organisms are organized across many spatial scales, yet existing, cost-effective imaging systems can measure only a subset of these scales at once. Here, we have created a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution recording from multiple spatial scales simultaneously, ranging from cellular structures to large-group behavioral dynamics. By collecting data from up to 96 cameras, we computationally generate gigapixel-scale images and movies near cellular resolution and 5 um sensitivity over hundreds of square centimeters. This allows us to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales, including larval zebrafish, fruit flies, nematodes, carpenter ants, and slime mold. The MCAM architecture allows stereoscopic tracking of the z-position of organisms using the overlapping field of view from adjacent cameras. Further, we demonstrate the ability to acquire dual color fluorescence video of multiple freely moving zebrafish, recording neural activity via ratiometric calcium imaging. Overall, the MCAM provides a powerful platform for investigating cellular and behavioral processes across a wide range of spatial scales, but without the bottlenecks imposed by single-camera image acquisition systems.