Publications

2025

"Serotonin modulates neural dynamics in a subspace orthogonal to the choice space," Guido T Meijer, et al. bioRxiv. posted 1 August 2025, 10.1101/2025.08.01.668048

"Spatially distributed and regionally unbound cellular resolution brain-wide processing loops in mice," Michael Schartner, et al. bioRxiv. posted 1 August 2025, 10.1101/2025.07.30.667641

"A common computational and neural anomaly across mouse models of autism," Jean-Paul Noel, et al., Nat Neurosci (2025). https://doi.org/10.1038/s41593-025-01965-8

"Reproducibility of in-vivo electrophysiological measurements in mice," The International Brain Laboratory et al., eLife 13:RP100840. https://doi.org/10.7554/eLife.100840.3

"Neural Encoding and Decoding at Scale," Yizi Zhang et al., Proceedings of the 42nd International Conference on Machine Learning, Vancouver, Canada. PMLR 267, 2025.

"In vivo cell-type and brain region classification via multimodal contrastive learning," Han Yu, et al. (2025); International Conference on Learning Representations (ICLR).

2024

"Internal states emerge early during learning of a perceptual decision-making task," Lenca I. Cuturela, The International Brain Laboratory and Jonathan W. Pillow, bioRxiv. posted 1 December 2024, 10.1101/2024.11.30.626182

"Exploiting correlations across trials and behavioral sessions to improve neural decoding,"Yizi Zhang et al., bioRxiv. posted 15 September 2024, 10.1101/2024.09.14.613047

"A study of animal action segmentation algorithms across supervised, unsupervised, and semi-supervised learning paradigms," Ari Blau, et al. Neurons, Behavior, Data Analysis, and Theory, December, 1–46. https:/​/​doi.org/​10.51628/​001c.127770

"Towards a "universal translator" for neural dynamics at single-cell, single-spike resolution,” Yizi Zhang, et al., Advances in Neural Information Processing Systems 37 (NeurIPS 2024)

"Interactive data exploration websites for large-scale electrophysiology," Daniel Birman et al., bioRxiv.posted 10 June 2024, 10.1101/2024.06.07.597950

"Parsing neural dynamics with infinite recurrent switching linear dynamical systems," Geadah V, et al., (2024). International Conference on Learning Representations (ICLR).

"Pre-existing visual responses in a projection-defined dopamine population explain individual learning trajectories," Alejandro Pan Vazquez, et al., Current Biology (2024), https://doi.org/10.1016/j.cub.2024.09.045

"Identifying the factors governing internal state switches during nonstationary sensory decision-making," Zeinab Mohammadi, et al., bioRxiv.posted 4 February 2024, 10.1101/2024.02.02.578482

2023

"Dissecting the Complexities of Learning With Infinite Hidden Markov Models," Sebastian A. Bruijns, et al., bioRxiv, https://doi.org/10.1101/2023.12.22.573001

"Bypassing spike sorting: Density-based decoding using spike localization from dense multielectrode probes," Yizi Zhang et al., Advances in Neural Information Processing Systems 36 (NeurIPS 2023)

"Pinpoint: trajectory planning for multi-probe electrophysiology and injections in an interactive web-based 3D environment," Daniel Birman, et al., bioRxiv, https://doi.org/10.1101/2023.07.14.548952

"A Brain-Wide Map of Neural Activity during Complex Behaviour," International Brain Laboratory et al, bioRxiv, https://doi.org/10.1101/2023.07.04.547681

"Brain-wide representations of prior information in mouse decision-making," Charles Findling et al., bioRxiv, https://doi.org/10.1101/2023.07.04.547684

"Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools," Dan Biderman et al., Nat Methods 21, 1316–1328 (2024). https://doi.org/10.1038/s41592-024-02319-1

"A modular architecture for organizing, processing and sharing neurophysiology data," The International Brain Laboratory et al., Nat Methods, https://doi.org/10.1038/s41592-022-01742-6

2022

"Mice alternate between discrete strategies during perceptual decision-making," Ashwood et al., Nat Neurosci. https://doi.org/10.1038/s41593-021-01007-z

2021

"Accurate localization of linear probe electrode arrays across multiple brains", Liu D Liu et al., eNeuro. 25 October 2021, ENEURO.0241-21.2021

"High-Performance Interactive Scientific Visualization With Datoviz via the Vulkan Low-Level GPU API", Cyrille Rossant et al., Computing in Science & Engineering, vol. 23, no. 04, pp. 85-90, 2021.

"Standardized and reproducible measurement of decision making in mice", The International Brain Laboratory et al., eLife 2021;10:e63711.

"Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders", Matt R. Whiteway et al., PLoS Comput Biol. 2021 Sep 22;17(9):e1009439.

"Decentralized motion inference and registration of Neuropixel data", Erdem Varol et al., IEEE International Conference on Acoustics, Speech and Signal Processing, 2021

"Extracting the Dynamics of Behavior in Decision-Making Experiments", Nicholas A. Roy et al., Neuron. 2021 Feb 17;109(4):597-610.e6.

"Citric Acid Water as an Alternative to Water Restriction for High-Yield Mouse Behavior", Anne E. Urai et al., eNeuro. 2021 Feb 11;8(1):ENEURO.0230-20.2020.

2020

"Knowledge across networks: how to build a global neuroscience collaboration”, Lauren Wool and The International Brain Laboratory, Current Opinion in Neurobiology, 65:100-107.

"Deep Graph Pose: a semi-supervised deep graphical model for improved animal pose tracking”, Anqi Wu et al., Advances in Neural Information Processing Systems 33

"Inferring learning rules from animal decision-making”, Zoe Ashwood et al., Advances in Neural Information Processing Systems 33 Advances in Neural Information Processing Systems 33

"Reverse-engineering Recurrent Neural Network solutions to a hierarchical inference task for mice", Rylan Schaeffer et al., Advances in Neural Information Processing Systems 33

2017

"An International Laboratory for Systems and Computational Neuroscience," The International Brain Laboratory. Neuron 96.6 (2017):1213-1218.  

White Paper

• IBL Video Data Analysis Pipeline

• IBL Spike Sorting Pipeline

Opinions

• "A conversation with research software engineers at the International Brain Laboratory," Mayo Faulkner, Miles Wells

• ”Accepting ‘the bitter lesson’ and embracing the brain’s complexity,” Eva Dyer, Blake Richards; Response from Gaelle Chapuis

• “Neuroscience needs a career path for software engineers,” Gaëlle Chapuis, Olivier Winter (Listen to this article read aloud)

• “Women are systematically under-cited in neuroscience. New tools can change that,” Anne Churchland, Felicia Davatolhagh.

Conference Abstracts

SfN 2023

• Universal Renderer for Neuroscience: interactive 3D rendering for electrophysiology and neuroimaging in the browser, on desktops, and in virtual reality

• Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open source tools

• Brain-wide atlas of electrophysiological properties and associated tools

• Automating multi-probe insertions to improve the efficiency and reproducibility of electrophysiology

  experiments

• Atlas of intrinsic timescales in the mouse brain

SfN 2022

• Basal ganglia and prethalamic pathways play disparate roles in sensory-guided decision-making

• Single-cell correlates of sensory, cognitive, and motor variables across the brain

• Serotonin modulates neural dynamics and inter-area communication across the mouse brain

• Multi-probe targeting for Neuropixels using interactive 3D visualizations and simulated electrophysiology

• International Brain Laboratory_ A Brian Wide Map of Neural Activity during Complex Behavior in Mice

• International Brain Laboratory brainwide analysis_ decoding of task and behavioral variables from populations of neurons

• International Brain Laboratory brain-wide-map analysis_ Standardized Euclidean distance of trial-averaged activity across neuropixel recordings reveals a graded response to task-relevant variables

• Encoding models reveal brain-wide signaling of motor activity and reward delivery

• Distributed neural representations of prior information in mouse decision-making

• Comparison of neuromodulator signaling in a visual decision-making task

SfN 2019

• Visual decision-making in a dynamically changing environment: comparing mouse behavior to ideal
  observer models

• Citric Acid water as an alternative to water scheduling in behaving mice

• State‐dependent modeling of psychophysical behavior during decision making

• The IBL data architecture: DataJoint pipeline

• The IBL data architecture: tools for storing and accessing diverse datasets collected at multiple
  sites

• Detecting information‐limiting noise correlations in early visual cortex

• The International Brain Laboratory: standardizing and reproducing a decision-making
  task in mice across laboratories

• Robust and generalizable tracking of body parts of head-fixed mice

SfN 2018

• The International Brain Laboratory: Reproducing a Single Decision-Making Behavior in Mice Across Labs

• The International Brain Laboratory: Data Architecture