Motilitometer: A compact modular microscope for motility and photoresponse analysis of microorganisms

In biology, cell motility is a valuable indicator, revealing how cells sense their environment, adapt to stimuli, and reflect their physiological state. In this paper, we present a modular microscopy system designed to study the motility of microorganisms. The setup is compact, assembled from low-cost 3D-printed and widely available components. It integrates programmable multispectral illumination to enable controlled photo stimulation and investigation of light-induced behavioral responses, including phototaxis. Initially developed for the investigation of photosynthetic microalgae, the system is easily adaptable to a wide range of motile microorganisms. It supports two complementary observation modes: a droplet-based chamber that minimizes sedimentation for cell speed analysis, and a deeper chamber that allows sedimentation, enabling quantitative assessment of motility fraction and orientation relative to directional light. The optical system provides a magnification of up to approximately 9×, sufficient for the precise centroid detection and tracking of single cells. This open-source, DIY (Do It Yourself) microscopy platform offers an accessible tool for photobiology, microbial ecology, and biophysics, helping democratize quantitative motility studies.