PeopleofSuperintelligence

Researcher

Fuhui Long

Fuhui Long is a researcher whose work applies machine learning and computer vision to biological imaging and neuroscience. At the Howard Hughes Medical Institute's Janelia Farm Research Campus, they built a 2009 3D digital atlas of Caenorhabditis elegans, coauthored V3D for real-time 3D microscopy in 2010, and developed the all-path pruning neuron-tracing algorithm in 2011. At the Allen Institute for Brain Science, they coauthored the open-source deep-learning neuron-tracing toolbox DeepNeuron in 2018 and a 2021 Nature survey of spiking across the mouse visual system. In 2026, they coauthored mouse-brain studies predicting more than 17.99 million post-synaptic sites and using NeuroXiv2 to integrate neuronal morphology, connectivity, and transcriptomic profiles across 1,385 brain regions.

Works
92

Publication numbers from OpenAlex, as of 22 October 2026. Citations and h-index are hidden because this OpenAlex record may be incomplete or mix in other authors.

Timeline

  1. 2007–2009

    Fly-embryo and worm atlases at Janelia

    At the Howard Hughes Medical Institute's Janelia Farm Research Campus in 2007, Long coauthors an automated image-analysis method for Drosophila melanogaster embryo gene-expression patterns and an algorithm that straightens curved Caenorhabditis elegans images using a parametric cubic spline backbone. As first author at Janelia in 2009, they build a 3D digital atlas of the C. elegans L1 larva that assigns cell names to 357 nuclei automatically with 86% accuracy.

  2. 2010

    V3D for 3D microscopy

    With Hanchuan Peng, Zongcai Ruan, Julie H. Simpson, and Eugene W. Myers at Janelia Farm Research Campus, Long coauthors V3D in 2010, a system that visualizes gigabyte-sized microscopy image stacks in real time on laptops and desktops. The team also builds V3D-Neuron to reconstruct 3D neuronal structures from high-resolution brain images.

  3. 2011

    All-path pruning for neuron tracing

    In 2011, Long coauthors all-path pruning (APP), an automatic graph algorithm that traces the 3D structure of a neuron.

  4. 2012

    A primer on 3D microscopy

    Working with Jianlong Zhou and Hanchuan Peng at Janelia Farm Research Campus in 2012, they publish a first-author educational primer in PLOS Computational Biology on 3D microscopic-image visualization and analysis. It covers segmentation, registration, and annotation, with examples from C. elegans and fruit-fly neurite tracts.

  5. 2018

    DeepNeuron for neuron tracing

    At the Allen Institute for Brain Science in Seattle, they coauthor DeepNeuron in 2018, an open-source toolbox that uses deep-learning networks to learn features and rules from data and trace neuron morphology in light-microscopy images.

  6. 2021

    A mouse visual-system survey

    They coauthor a 2021 Nature study at the Allen Institute for Brain Science that surveys spiking from tens of thousands of units across six cortical and two thalamic regions in mice responding to visual stimuli. Cross-correlation analysis finds that functional connectivity during visual stimulation mirrors the anatomical hierarchy.

  7. February 2026

    Predicted post-synaptic sites

    In February 2026, they coauthor a study that uses a statistical approach based on potential arbor contacts to generate more than 17.99 million predicted post-synaptic sites across the dendritic arbors of 155,743 mouse-brain neurons. The analysis links the sites' spatial distribution with electrophysiological activity and gene-expression data.

  8. March 2026

    Multimodal mouse-brain analysis with NeuroXiv2

    In March 2026, Long coauthors a study on AI-driven analysis of mouse-brain data, using NeuroXiv2 to integrate neuronal morphology, connectivity, and transcriptomic profiles across 1,385 hierarchical brain regions, 182,483 reconstructed neurons, and 5.24 million cells with expression data for 1,122 genes.

  1. The company share of AI researchers’ top papers was 31% in 2020–2024 and 8% in 1970–1974Includes Allen Institute for AI (Ai2). We estimate where the people shaping AI worked when their most-cited papers appeared: the company share was 31% in 2020–2024 and 8% in 1970–1974, and Google led all organizations in 2020–2024.
  2. Companies supply the most prior-work hires at 7 of the 9 frontier AI labsIncludes Allen Institute for AI (Ai2). Our estimates of the organizations where 550 people worked directly before joining 9 frontier AI labs across 620 career transitions, comparing the main feeder organizations per lab.
  3. 72% of AI researchers with top works connect into a single 2,592-person co-author groupIncludes Allen Institute for AI (Ai2). We map the co-author network across 3,593 people shaping AI and 14,977 most-cited papers: 2,592 (72%) form one connected group with a median distance of 5 steps, led in 2-step reach by Yoshua Bengio (570) and in shortest-path bridging by Yoshua Bengio (6.7%).
  4. Direct Form 990 pay in the latest returns of 39 nonprofits with AI people on this site is highest at $2.1M at the Allen Institute for AI (Ai2) (2024)Includes Allen Institute for AI (Ai2). IRS Form 990 compensation across 39 nonprofits with AI people on this site from 2012 to 2025: in the latest returns, Mozilla reports $6.1M including related-company pay (2024) and the Allen Institute for AI (Ai2) leads direct nonprofit pay at $2.1M (2024).

Sources and credits

Photo: We have no published photo of Fuhui Long yet. Send us a free-licensed photo.

  1. Automatic image analysis for gene expression patterns of fly embryos - PMC pmc.ncbi.nlm.nih.gov. Checked 22 October 2026.
  2. Straightening Caenorhabditis elegans images - PMC pmc.ncbi.nlm.nih.gov. Checked 22 October 2026.
  3. A 3D Digital Atlas of C. elegans and Its Application To Single-Cell Analyses - PMC pmc.ncbi.nlm.nih.gov. Checked 22 October 2026.
  4. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets nature.com. Checked 22 October 2026.
  5. Automatic 3D neuron tracing using all-path pruning - PMC pmc.ncbi.nlm.nih.gov. Checked 22 October 2026.
  6. Visualization and Analysis of 3D Microscopic Images | PLOS Computational Biology journals.plos.org. Checked 22 October 2026.
  7. DeepNeuron: an open deep learning toolbox for neuron tracing - PMC pmc.ncbi.nlm.nih.gov. Checked 22 October 2026.
  8. Survey of spiking in the mouse visual system reveals functional hierarchy - PMC pmc.ncbi.nlm.nih.gov. Checked 22 October 2026.
  9. Brain-wide Organization of Post-Synaptic Sites: Three Principles researchsquare.com. Checked 22 October 2026.
  10. Semi-Independent Transcriptomic, Morphological, Connectivity Dimensions of the Mouse Brain Revealed by CoT-Mining 258 Million Multimodal Associations researchsquare.com. Checked 22 October 2026.