Agent-Lens — AI Agents for Smart Microscopy

What if you could run a microscope just by describing what you want to see? Agent-Lens is a web-based platform where an AI agent turns natural-language intent — “scan well C3 and find the cells with strong green fluorescence” — into concrete microscope commands. It brings together hardware control, time-lapse imaging, segmentation (SAM), and similarity search (CLIP/DINOv2) behind a single conversational interface.

Built on Hypha, Agent-Lens connects instruments, AI models, and an interactive UI into one workspace, and manages large image datasets in OME-Zarr. It is our step toward self-driving microscopy: experiments that observe, decide, and adapt on their own, so biologists can focus on the questions instead of the controls.