Fuming (Felix) Yang

fumingyang@fas.harvard.edu

Cambridge, MA 02138

Hi! I’m Fuming (Felix) Yang, a Research Fellow in the Lichtman Lab at Harvard University.

Research Interests

My research interests center on using AI/ML methods to build high-throughput imaging pipelines and on understanding how to extract biological insights from large brain datasets, while letting those insights, in turn, inform advances in AI/ML.

Current Work

I currently lead data-acquisition efforts at an electron microscopy facility at Harvard, funded by NIH-UM1 award as part of the High-throughput Integrative Mouse Connectomics (HI-MC) project—a collaboration between Harvard, Princeton, Google, MIT, the Allen Institute, the University of Cambridge, and Johns Hopkins University. Our goal is to reconstruct 10 mm³ of adult mouse cortex at nanometer resolution (~20 PB of data). I build, operate, and optimize the imaging pipeline, develop high-throughput quality-control workflows, and carry out downstream analyses. The pipeline combines a custom tissue mill with a 91-beam scanning electron microscope (Zeiss MultiSEM) to enable automated, record-speed imaging of large neural volumes.

Research Areas

Computer Vision & ML: Graph theory, image compression, 2D/3D reconstruction, NN architecture
Neuroscience: Connectomics, developmental neuroscience, synapses elimination
Software & Tools: High-throughput imaging pipelines, automated acqusition/QC workflows

“Shoot for the moon. Even if you miss, you land among stars”

news

Jan 13, 2026	🎉 Two papers accepted to ISBI 2026! Towards 1000-Fold Electron Microscopy Image Compression for Connectomics via VQ-VAE with Transformer Prior and WaferTools: A Software for Section Segmentation, ROI Registration, and Section Ordering!
Nov 24, 2025	🎉 DRIFT-EM: Direct retrieval of ultrathin serial sections by ionizer-facilitated transfer for volume electron microscopy submitting to Cell Reports Methods!
Nov 8, 2025	🎉 WaferTools - Software for Wafer-related Automatic Methods in Connectomics. submitted to ISBI 2026!
Oct 31, 2025	🏆 Our Project (Bio-inspired AI) has been nominated by Harvard University for the Kempner Institute Accelerator Award recognizing novel AI/ML methods, grateful to all collaborators!
Oct 31, 2025	🎉 Towards 1000-fold Electron Microscopy Image Compression for Connectomics via VQ-VAE with Transformer Prior submitted to arXiv and ISBI 2026!
Sep 30, 2025	🎉 Neuromuscular connectomes across development reveal synaptic ordering rules got accepted by Nature Neuroscience! Huge milestone for the team!
Sep 26, 2025	🎉 Budgeted Broadcast: An Activity-Dependent Pruning Rule for Neural Network Efficiency submitted to ICLR 2026!
Sep 16, 2025	🎉 Developmental Connectomics of the Mouse Cerebellum is submitting to Nature!
Sep 7, 2025	🎉 Sparse Graph Reconstruction and Seriation for Large-Scale Image Stacks submitted to arXiv!
May 9, 2025	🎉 Joined Lichtman Lab at Harvard University as a Research Fellow!
Aug 30, 2024	🏆 Department Head’s Fellowship and Academic Excellence Fellowship from Carnegie Mellon University!

selected publications

MICCAI

Sparse Graph Reconstruction and Seriation for Large-Scale Image Stacks

Fuming Yang, Yaron Meirovitch, and Jeff W. Lichtman

MICCAI (submitting) - ArXiv preprint, 2025

arXiv Bib Code YouTube

@article{yang2025seriation,
  title = {Sparse Graph Reconstruction and Seriation for Large-Scale Image Stacks},
  author = {Yang, Fuming and Meirovitch, Yaron and Lichtman, Jeff W.},
  journal = {MICCAI (submitting) - ArXiv preprint},
  year = {2025},
  youtube = {https://youtu.be/f8raYfpha_k},
  benchmark = {https://github.com/FumingYang-Felix/Graph-Condensation-Densification-and-SuperChain-for-1D-Seriation/releases/tag/Benchmark},
}

ISBI

Towards 1000-fold Electron Microscopy Image Compression for Connectomics via VQ-VAE with Transformer Prior

Fuming Yang, Yicong Li, Hanspeter Pfister, and 2 more authors

ISBI (in press) - ArXiv preprint, 2025

arXiv Bib Code YouTube

@article{yang2025compression,
  title = {Towards 1000-fold Electron Microscopy Image Compression for Connectomics via VQ-VAE with Transformer Prior},
  author = {Yang, Fuming and Li, Yicong and Pfister, Hanspeter and Lichtman, Jeff W. and Meirovitch, Yaron},
  journal = {ISBI (in press) - ArXiv preprint},
  year = {2025},
  youtube = {https://www.youtube.com/watch?v=1rl-LlP0kVc},
}

ICLR

Budgeted Broadcast: An Activity-Dependent Pruning Rule for Neural Network Efficiency

Yaron Meirovitch*, Fuming Yang*, Jeff W. Lichtman, and 1 more author

ICLR (under review) - ArXiv preprint, 2025

*Equal contribution

arXiv Bib Code YouTube

@article{meirovitch2025budgeted,
  title = {Budgeted Broadcast: An Activity-Dependent Pruning Rule for Neural Network Efficiency},
  author = {Meirovitch*, Yaron and Yang*, Fuming and Lichtman, Jeff W. and Shavit, Nir},
  journal = {ICLR (under review) - ArXiv preprint},
  year = {2025},
  note = {*Equal contribution},
  youtube = {https://www.youtube.com/watch?v=xhxaWfZQG6c},
}

ISBI

Software for Wafer-related Automatic Methods in Connectomics

Fuming Yang, Yaron Meirovitch, Frederico Araújo, and 3 more authors

ISBI (in press), 2025

Bib Code YouTube

@article{yang2025wafertools,
  title = {Software for Wafer-related Automatic Methods in Connectomics},
  author = {Yang, Fuming and Meirovitch, Yaron and Araújo, Frederico and Schalek, Richard and Susoy, Vald and Lichtman, Jeff W.},
  journal = {ISBI (in press)},
  year = {2025},
  youtube = {https://www.youtube.com/watch?v=UsmY64RtiGQ},
}

Nat Neurosci

Neuromuscular connectomes across development reveal synaptic ordering rules

Yaron Meirovitch, Kai Kang, Ryan W. Draft, and 12 more authors

Nature Neuroscience (in press), 2025

Bib HTML PDF

@article{meirovitch2025neuromuscular,
  title = {Neuromuscular connectomes across development reveal synaptic ordering rules},
  author = {Meirovitch, Yaron and Kang, Kai and Draft, Ryan W. and Pavarino, Elisa C. Pavarino and Echeverri, Maria Fernanda and Yang, Fuming and Turney, Stephen G. and Berger, Daniel R. and Peleg, Adi and Montero-Crespo, Marta and Schalek, Richard L. and Lu, Ju and Livet, Jean and Tapia, Juan Carlos and Lichtman, Jeff W.},
  journal = {Nature Neuroscience (in press)},
  year = {2025},
}

Cell Rep

DRIFT-EM: Direct retrieval of ultrathin serial sections by ionizer-facilitated transfer for volume electron microscopy

Nelson Medina, Joseph V Gogola, Kevin Boergens, and 5 more authors

Cell Reports Methods(under review), 2025

Bib

@article{medina2025driftem,
  title = {DRIFT-EM: Direct retrieval of ultrathin serial sections by ionizer-facilitated transfer for volume electron microscopy},
  author = {Medina, Nelson and Gogola, Joseph V and Boergens, Kevin and Yang, Fuming and Meirovitch, Yaron and Lichtman, Jeff W. and Kasthuri, Narayanan and Wildenberg, Gregg},
  journal = {Cell Reports Methods(under review)},
  year = {2025},
}