Seung Lab

Princeton Neuroscience Institute

Welcome to the Connectomic Era

The first neuronal wiring diagram for a brain was recently released, and has leaped orders of magnitude beyond the 1986 wiring diagram of the C. elegans nervous system. This historic milestone showcases the revolutionary progress achieved in EM image acquisition and analysis over the past decade. The connectomic era has finally begun.

The Seung lab first applied convolutional nets to EM image analysis in 2007, and continued development of this approach resulted in the fly connectome and a wiring diagram of a cortical column . Now we are passing the baton to Zetta AI , which will continue innovating to create the artificial intelligence required to scale up connectomics to a mouse brain and beyond.

The Seung lab has shut down its EM image analysis effort, and refocused on making discoveries about brain function, as well as brain development and plasticity.

Our Research

Interpretation of connectomes

We are devising concepts and methods for interpreting neuronal wiring diagrams. The fly connectome includes as a corollary the first wiring diagram of a visual system. By studying this wiring diagram, we have discovered a new circuit for form vision in the fly brain. We have also discovered that many inhibitory interneuron types function as a highly diverse set of normalization mechanisms in fly vision. Both of these discoveries draw on the striking analogy between the fly visual system and convolutional nets.

Reconstructing neural circuits

In ongoing collaborations, we are applying and refining connectomic technologies to reconstruct more fly connectomes (Mala Murthy), as well as a patch of mouse retina (Thomas Euler). We are reconstructing mouse neural circuits for memory (David Tank), decision making (Adrian Wanner and Jeff Lichtman), and reinforcement learning (Ilana Witten). These collaborations make use of the high throughput EM facility at the Princeton Neuroscience Institute. In many of the projects, neural circuit reconstruction is preceded by calcium imaging of neural activity in vivo.

Scaling up to mammalian brains

Today's connectomic technologies are sufficient for reconstructing an entire fly brain, and are also being applied to millimeter-scale chunks of mammalian brains . A mouse brain is 1000× larger, and a human brain 1000× larger still. There is plenty of room at the top. We are participating in a "transformative project" of the NIH BRAIN Initiative that aims to scale up connectomics to a whole mouse brain. The Princeton Neuroscience Institute is the only site in the world with both of the EM image acquisition technologies that are being scaled up to the mouse connectome, beam-deflection transmission electron microscopy and multi-beam scanning electron microscopy .

Scaling down to molecules

The fly connectome was reconstructed from EM images with 4×4×40 nm³ voxels, which is sufficient for detecting chemical synapses and tracing the "wires" of the brain. This resolution might seem very fine, but is actually coarse compared to the 0.1 nm theoretical limit of EM. There is plenty of room at the bottom. Serial section EM tomography can improve resolution; the challenge is to deliver this improvement over much larger volumes than before. One can imagine, for example, imaging an entire fly brain at 4×4×4 nm³ or 2×2×2 nm³ resolution. This would reveal brain cell biology in fantastic detail, within the full context of neurons and their connections.

Highlighted Publications

Our Team

Principal Investigator

Prof. Sebastian Seung

Princeton Neuroscience Institute and Department of Computer Science

Postdoctoral Researchers

  • Ran Lu, Princeton Neuroscience Institute
  • Zhihao Zheng, Princeton Neuroscience Institute
  • Changjoo Park, Princeton Neuroscience Institute
  • Yannan Chen, Princeton Neuroscience Institute
  • Chris Salmon, Princeton Neuroscience Institute

Graduate Students

  • Eric Hammerschmith, Princeton Neuroscience Institute

Staff

  • Arie Matsliah, Research Software Engineer and Data Evangelist, FlyWire (Joint with Murthy Lab)
  • Sebastian Ströh, EM Facility Manager
  • William Silversmith, Software Developer
  • Ryan Morey, Software Developer
  • Chris Jordan, Software Developer
  • Raghav Navaratna, Robotics Automation Engineer
  • Clayton Donhauser, Robotics Vision Engineer
  • Steven Sokalski, Instrumentation Engineer (Joint with Tank Lab)
  • Amy Sterling, Crowdsourcing & Outreach Manager
  • May Husseini, Connectomics Manager

Image Analysts

  • Ben Silverman, Tracer
  • Jay Gager, Tracer
  • Kyle P. Willie, Tracer
  • Ryan Willie, Tracer
  • Douglas Bland, Tracer
  • Austin Burke, Tracer
  • James Hebditch, Tracer
  • Marissa Sorek, Game Master
  • Celia David, Game Master
    • Lab Alums
    • Sven Dorkenwald, Postdoc Researcher, Computer Science, Princeton University
    • Kyle Luther, Postdoc Researcher
    • Claire McKellar, Research Scholar
    • Ashwin Vishwanathan, Postdoc Researcher
    • Shang Mu, Postdoc Researcher
    • Jingpeng Wu, Postdoc Researcher
    • Kisuk Lee, Postdoc Researcher
    • Adrian Wanner, Postdoc Researcher
    • Alyssa Wilson, Postoc Researcher
    • Zhen Jia, Postdoc Researcher
    • Mu Qiao, Postdoc Researcher
    • Jinseop Kim, Postdoc Researcher
    • Daniel Berger, Postdoc Researcher
    • Ignacio Arganda-Carreras, Postdoc Researcher
    • Runzhe Yang, Graduate Student, Computer Science, Princeton University
    • Thomas Macrina, Graduate Student, Computer Science, Princeton University
    • Sergiy Popovych, Computer Science, Computer Science, Princeton University
    • Nicholas Turner, Graduate Student, Computer Science, Princeton University
    • J. Alexander Bae, Graduate Student, Electrical Engineering, Princeton University
    • Karan Kathpalia, Graduate Student, Computer Science, Princeton University
    • Davit Buniatyan, Graduate Student, Computer Science, Princeton University
    • Zoe Ashwood, Graduate Student, Princeton University
    • Aleksandar Zlateski, Graduate Student, Electrical Engineering & Computer Science, Massachusetts Institute of Technology
    • Matt Greene, Graduate Student, Brain & Cognitive Sciences, Massachusetts Institute of Technology
    • Sachin Ravi, Graduate Student, Computer Science, Princeton University
    • Jonathan Zung, Graduate Student, Computer Science, Princeton University
    • Szi-chieh Yu, Image Analyst Manager
    • Akhilesh Halageri, Software Developer
    • Kai Kuehner, Software Developer
    • Nico Kemnitz, Developer
    • Barak Nehoran, Developer
    • Manuel Castro, Developer
    • William Wong, Developer
    • Dodam Ih, Developer
    • Ignacio Tartavull, Developer
    • Seun (Oluwaseun) Ogedengbe, Software Developer
    • Raphael Levisse, Research Programmer
    • Devon Jones, Game Master
    • Mio Akasako, Research Technician
    • Katherine Nelson, Research Technician
    • Matt Susskind, Undergraduate, Massachusetts Institute of Technology
    • Curtis Belmonte, Undergraduate, Computer Science, Princeton University
    • Elias Wang, Intern
    • Jegug Ih, Intern
    • Alex Norton, Graphic Designer
    • Rachel Prentki, Tracer
    • Sarah Morejohn, Tracer
    • Selden Koolman, Tracer
    • Merlin Moore, Tracer
    • Rob Hamill, Graphic Designer
    • Daniela Gamba, Game Master
    Older Lab Alums
    • Daan Visser
    • Michael Weiss
    • Uygar Sümbül
    • Heather Sullivan
    • Amy Dunn
    • Viren Jain
    • Neville Sanjana
    • Sen Song
    • Srinivas Turaga
    • Kannan U V
    • Jen Wang
    • Ian Wickersham
    • Seleeke Flingai
    • Steven (Zi) Ji
    • Rachel Shearer
    • Brett Warne
    • Jan Rodriguez
    • Aaron Hammond
    • Barbara Duckworth
    • David Wong
    • Jason Toy

    Contact Us

    Sebastian Seung: sseung@princeton.edu
    153 Princeton Neuroscience Institute | 40 Woodlands Way | Princeton, NJ 08544


    May Husseini: mayh@princeton.edu
    280 Princeton Neuroscience Institute | 40 Woodlands Way | Princeton, NJ 08544


    Princeton Neuroscience Institute on Google Maps

    Visiting Princeton University

    Campus Interactive Map