The program
AI-in-the-Loop Discovery
AI-in-the-Loop is a new mode of research in which scientists’ expertise and AI’s analytical power operate in a continuous loop, driving discovery at a speed and scale beyond anything biology’s seen before. Broadly, AI systems analyze complex data, build models, and help design tools, systems, and automated pipelines. Scientists and AI co-create hypotheses and experimental strategies. Scientists run experiments, make decisions, and collect high-dimensional data. AI learns from that large-scale data and the cycle repeats.
This is the methodology HHMI is committed to building. Where the underlying AI capabilities are mature, we use them. Where they are not, we advance them, working through AI@HHMIexternal link, opens in a new tab — our institutional commitment to artificial intelligence in biological research — and in close collaboration with Google and Anthropic.
Model Organisms
Fruit fly
Complete neural map
Janelia has decades of experience with the fruit fly. In 2020 it published the fly “hemibrain” connectome — then the largest and most detailed synaptic-level brain map ever produced — and in 2025 the first complete connectome of a male fruit fly’s entire central nervous system, brain and nerve cord together. With a brain wiring map of roughly 140,000 neurons, a precise genetic toolkit, and Janelia’s dedicated fly labs, the fruit fly is where we develop AI-in-the-Loop Discovery and our integrated molecular workflows.
Larval zebrafish
Whole-brain imaging
The larval zebrafish is the only vertebrate in which every neuron in the brain can be imaged at once during behavior, and it’s where we’ll build the whole-brain pipeline the adult Danionella platform will need. Our zebrafish work has already uncovered fundamental principles underlying sensorimotor processing and motor learning while pushing the boundaries of imaging technology. This is where whole-brain neuroscience becomes possible, and where we learn to scale it.
Danionella
Whole-organism vertebrate platform
Because Danionella remains transparent throughout its life, it allows Janelia scientists to work toward what’s never been possible in an adult vertebrate before: imaging the whole brain in a living animal during natural, complex behavior. That opens a path that larval systems alone can’t provide — toward recording, mapping, and ultimately understanding how biology becomes behavior. Over the coming decade, Danionella is where we pursue that understanding in full.