MouseConnects Complete Hippocampal Connectome
A synapse-level reconstruction of 10 mm³ of the mouse hippocampal formation – revolutionizing our understanding of memory circuits.
Revolutionary Scale & Impact
MouseConnects represents a quantum leap in connectomics, targeting the mouse hippocampal formation - the brain region essential for memory formation and spatial navigation. This project will generate the first complete synaptic wiring diagram of a mammalian memory circuit.
Key Innovations
- Novel mSEM-IBEAM Technology: Combines multibeam electron microscopy with ion beam milling
- Distributed Imaging: Multiple sites working in parallel for unprecedented speed
- AI-Powered Reconstruction: State-of-the-art machine learning for automated segmentation
- Open Science: All data and tools freely available to the global research community
Scientific Questions Addressed
- How do hippocampal circuits encode spatial information and episodic memories?
- What are the detailed microcircuit motifs underlying grid and place cell function?
- How do different cell types contribute to memory formation and retrieval?
- What circuit principles enable the hippocampus to act as a cognitive map?
Cutting-Edge Technology Stack
mSEM-IBEAM Imaging
91-beam scanning electron microscopy combined with ion beam milling for automated blockface imaging at unprecedented scale.
- Two imaging sites: Harvard & Princeton
- Automated wafer handling
- Real-time quality monitoring
Google Cloud Processing
Massive-scale data processing using Google's cloud infrastructure for alignment, segmentation, and analysis.
- Flood-filling networks for neuron tracing
- Automated synapse detection
- Real-time collaborative proofreading
Multi-Modal Integration
Combining EM data with Patch-seq recordings, fMOST morphology, and transcriptomic cell typing.
- 4,000+ Patch-seq recordings
- Whole-brain fMOST reconstructions
- Cross-modal cell type matching
World-Class Collaborative Team
🏛️ Harvard University
Jeff Lichtman, PI
Sample preparation and imaging expertise with decades of connectomics experience
🎓 Princeton University
Sebastian Seung & David Tank
mSEM imaging technology and deep learning algorithms for automated reconstruction
☁️ Google Research
Viren Jain
Cloud-scale processing infrastructure and machine learning segmentation algorithms
🧮 MIT
Ila Fiete
Circuit analysis, computational modeling, and theoretical frameworks for spatial coding
🧠 Allen Institute
Hongkui Zeng
Patch-seq recordings, transcriptomic cell typing, and multi-modal data integration
🔬 University of Cambridge
Gregory Jefferis
Data integration, analysis pipelines, and connectome interpretation methods
🚀 Johns Hopkins APL
William Gray-Roncal
Connectome quality assurance, community training, and data dissemination
Data Release Coming Soon
The MouseConnects dataset is currently in active development. Data release, interactive browsers, and analysis tools will be made available as the project progresses. Stay tuned for updates!