The paper presents the complete connectome of the Drosophila male central nervous system and compares it to the female connectome, identifying sex-specific and dimorphic neuronal types.

Cell · Sep 1, 2026Peer-reviewedNeuroscience

Connectome-driven neural inventory of a complete visual system

Aljoscha Nern, Frank Loesche, Shin-ya Takemura, Laura E. Burnett, Marisa Dreher, Eyal Gruntman, Judith Hoeller, Gary B. Huang, Michał Januszewski, Nathan C Klapoetke, Sanna Koskela, Kit D. Longden, Zhiyuan Lu, Stephan Preibisch, Wei Qiu, , Michael B. Reiser

A FIB-SEM connectome of the male Drosophila right optic lobe sorts ∼53,000 neurons into 727 types, with neurotransmitter predictions and 577 matched split-GAL4 lines.

Nature · Mar 26, 2025Peer-reviewedNeuroscience✦ In-depth digest

Periodic ER-plasma membrane junctions support long-range Ca2+ signal integration in dendrites

Lorena Benedetti, Ruolin Fan, Aubrey V. Weigel, Andrew S. Moore, Patrick R. Houlihan, Mark Kittisopikul, Grace Park, Alyson Petruncio, Philip M. Hubbard, Song Pang, C. Shan Xu, Harald F. Hess, Stephan Saalfeld, Vidhya Rangaraju, David E. Clapham, , Jennifer Lippincott‐Schwartz

The paper identifies periodic ER-PM junctions in dendrites that enable long-range Ca2+ signal integration through local spine activation and ryanodine receptor-dependent Ca2+ release.

Cell · Dec 20, 2024Peer-reviewedNeuroscience

NeuronBridge: an intuitive web application for neuronal morphology search across large data sets

Jody Clements, Cristian Goina, Philip M. Hubbard, Takashi Kawase, Donald J. Olbris, Hideo Otsuna, Robert Svirskas, Konrad Rokicki

NeuronBridge enables rapid morphological matching of neurons across large datasets imaged with different modalities.

BMC Bioinformatics · Mar 15, 2024Peer-reviewedNeuroscience

A Connectome of the Male Drosophila Ventral Nerve Cord

Shin-ya Takemura, Kenneth J. Hayworth, Gary B. Huang, Michał Januszewski, Zhiyuan Lu, Elizabeth C. Marin, Stephan Preibisch, C. Shan Xu, John Bogovic, Andrew S Champion, Han SJ Cheong, Marta Costa, Katharina Eichler, William T. Katz, Christopher J. Knecht, , Stuart Berg

Roughly 23 thousand traced neurons and 10 million TBars of the male Drosophila nerve cord, reconstructed from electron microscopy, typed, and queryable in neuPrint down to motor neurons.

bioRxiv · Jun 5, 2023 · PreprintNeuroscience✦ In-depth digest

Maintaining a stable head direction representation in naturalistic visual environments

Hannah Haberkern, Shivam S. Chitnis, Philip M. Hubbard, Tobias Goulet, Ann M. Hermundstad, Vivek Jayaraman

The paper shows that Drosophila maintains a stable head direction representation in naturalistic environments by tethering to global cues, even when local landmarks create potential conflicts.

bioRxiv · May 17, 2022 · PreprintNeuroscience

A Connectome and Analysis of the Adult Drosophila Central Brain

Louis K. Scheffer, C. Shan Xu, Michał Januszewski, Zhiyuan Lu, Shin-ya Takemura, Kenneth J. Hayworth, Gary B. Huang, Kazunori Shinomiya, Jeremy Maitin-Shepard, Stuart Berg, Jody Clements, Philip M. Hubbard, William T. Katz, Lowell A. Umayam, Ting Zhao, , Gregory S.X.E. Jefferis

The paper presents a detailed connectome of the adult Drosophila central brain, including new methods for data analysis and biological insights into neural circuit organization.

eLife · Sep 3, 2020Peer-reviewedBioinformatics

A Connectome of the Adult Drosophila Central Brain

C. Shan Xu, Michał Januszewski, Zhiyuan Lu, Shin-ya Takemura, Kenneth J. Hayworth, Gary B. Huang, Kazunori Shinomiya, Jeremy Maitin-Shepard, David Ackerman, Stuart Berg, Tim M. Blakely, John Bogovic, Jody Clements, Tom Dolafi, Philip M. Hubbard, , Ian A. Meinertzhagen

A dense electron-microscopy reconstruction of half the fly central brain, with nearly every cell typed and queryable online, turns months of tracing partners into a database lookup.

bioRxiv · Jan 21, 2020 · PreprintNeuroscience✦ In-depth digest

Accelerated EM Connectome Reconstruction using 3D Visualization and Segmentation Graphs

Philip M. Hubbard, Stuart Berg, Ting Zhao, Donald J. Olbris, Lowell A. Umayam, Jeremy Maitin-Shepard, Michał Januszewski, William T. Katz, Erika R. Neace, Stephen M. Plaza

This paper introduces semi-automated strategies combining 3D visualization and machine guidance to accelerate EM connectome reconstruction, showing improved performance over prior methods.

bioRxiv · Jan 17, 2020 · PreprintNeuroscience