the-enigma-project/omnimouse-dataset

OmniMouse dataset

Repository for the complete OmniMouse dataset.

The OmniMouse dataset comprises >2.3 million single-neuron recordings from visual cortex in 78 mice across 328 sessions, capturing >150 billion neural tokens during presentations of natural movies, natural images, parametric stimuli, and aligned behavioral measurements.

Currently, 68 sessions from 12 animals are withheld from this release pending an update to the orientation map preprint (Fahey et al., 2019); the withheld scans will be added shortly.

For more information, see the OmniMouse paper.

Additional resources

We provide Experanto, a Python package for working with neuroscience experiments and loading them into torch (including interpolation utilities for recordings and stimuli). Experanto is fully compatible with the Omnimouse data format out of the box and is highly recommended.

We also provide the Sensorium 2023 codebase and the OmniMouse codebase, which include tutorial notebooks and baseline models to help you get started.

Sample download

The following Python script demonstrates how to download a single experiment from the dataset.

1. Set the environment variable HF_TOKEN to your Hugging Face access token.
2. Run the script in a suitable Python environment (with huggingface_hub installed).

import os
import tarfile
from pathlib import Path
from huggingface_hub import hf_hub_download

# =========================
# Configuration
# =========================
HF_TOKEN = os.environ.get("HF_TOKEN")
REPO_ID = "the-enigma-project/omnimouse-dataset"

# Where you want the extracted experiment locally
DOWNLOAD_DIR = Path("data")

# Path of the tar file inside the HF repo
REMOTE_TAR_PATH = "experiments/dynamic17797-4-7-Video-021a75e56847d574b9acbcc06c675055_30hz.tar"


def test_download_and_extract():
    print(f"--- Starting download test from {REPO_ID} ---")

    try:
        DOWNLOAD_DIR.mkdir(parents=True, exist_ok=True)

        tar_local_path = hf_hub_download(
            repo_id=REPO_ID,
            repo_type="dataset",
            filename=REMOTE_TAR_PATH,
            token=HF_TOKEN,
            local_dir=DOWNLOAD_DIR,
        )

        tar_local_path = Path(tar_local_path)
        print(f"Downloaded tar to: {tar_local_path}")

        print("Extracting archive...")
        with tarfile.open(tar_local_path, "r") as tar:
            tar.extractall(path=DOWNLOAD_DIR)

        extracted_root = DOWNLOAD_DIR / tar_local_path.stem
        print(f"Extraction complete.")
        print(f"Experiment folder available at: {extracted_root}")

    except Exception as e:
        print(f"An error occurred during download or extraction: {e}")


if __name__ == "__main__":
    test_download_and_extract()

For a more detailed and customizable download script checkout the download_dataset.py file uploaded in this repo. For further guidance on downloading larger subsets (or the full dataset), see the Hugging Face Hub download documentation.

Authors

Paul G. Fahey^1,2,3,4, Kayla Ponder^*,1,2,3,4, Taliah Muhammad^*,1, Rachel Froebe^1,2,3,4, Lydia Ntanavara^1,2,3,4, Zheng H. Tan^1,2,3,4, Saumil Patel^1,2,3,4, Erick Cobos¹, Zhiwei Ding¹, Jiakun Fu^1,14, Zhuokun Ding^1,2,3,4, Dat Tran¹, Stelios Papadopoulos^1,2,3,4, Eric Y. Wang¹, Polina Turishcheva⁵, Konstantin Willeke^2,3,4,5, Christos Papadopoulos¹, Dimitri Yatsenko^1,7, Cameron Smith¹, Pawel A. Pierzchlewicz⁵, Tom Olschewski⁵, René Burghardt⁵, Yongrong Qiu^2,3,4,5, Sophia Sanborn^2,3,4, Xaq Pitkow^1,12,13, Katrin Franke^1,2,3,4, Edgar Y. Walker^1,10,11, Emmanouil Froudarakis^1,8,9, Jacob Reimer¹, Alexander S. Ecker^5,6, Fabian H. Sinz^1,5, Andreas S. Tolias^1,2,3,4,15

^* These authors contributed equally.

Affiliations

¹ Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA ² Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Stanford, CA, USA ³ Stanford Bio-X, Stanford University, Stanford, CA, USA ⁴ Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA ⁵ Institute of Computer Science and Campus Institute Data Science, University of Göttingen, Göttingen, Germany ⁶ Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany ⁷ DataJoint, Houston, TX, USA ⁸ Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, Greece ⁹ Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece ¹⁰ Department of Neurobiology and Biophysics, University of Washington, Seattle, WA, USA ¹¹ Computational Neuroscience Center, University of Washington, Seattle, WA, USA ¹² Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA, USA ¹³ Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA, USA ¹⁴ Salk Institute for Biological Studies, La Jolla, CA, USA ¹⁵ Department of Electrical Engineering, Stanford University, Stanford, CA, USA

Author Contributions

Within each category, initials are listed in alphabetical order by last name.

Initials key: E.C. = Erick Cobos; Zhiwei Ding = Zhiwei Ding; Zhuokun Ding = Zhuokun Ding; A.S.E. = Alexander S. Ecker; P.G.F. = Paul G. Fahey; K.F. = Katrin Franke; R.F. = Rachel Froebe; E.F. = Emmanouil Froudarakis; J.F. = Jiakun Fu; T.M. = Taliah Muhammad; L.N. = Lydia Ntanavara; C. Papadopoulos = Christos Papadopoulos; S. Papadopoulos = Stelios Papadopoulos; S. Patel = Saumil Patel; P.A.P. = Pawel A. Pierzchlewicz; X.P. = Xaq Pitkow; K.P. = Kayla Ponder; Y.Q. = Yongrong Qiu; J.R. = Jacob Reimer; S.S. = Sophia Sanborn; F.H.S. = Fabian H. Sinz; C.S. = Cameron Smith; Z.H.T. = Zheng H. Tan; A.S.T. = Andreas S. Tolias; D.T. = Dat Tran; P.T. = Polina Turishcheva; E.Y. Walker = Edgar Y. Walker; E.Y. Wang = Eric Y. Wang; K.W. = Konstantin Willeke; D.Y. = Dimitri Yatsenko; T.O. = Tom Olschewski; R.B. = René Burghardt

Conceptualization: E.C., Zhiwei Ding, Zhuokun Ding, A.S.E., P.G.F., K.F., E.F., J.F., S. Papadopoulos, S. Patel, P.A.P., X.P., J.R., S.S., F.H.S., C.S., A.S.T., D.T., P.T., E.Y. Walker, E.Y. Wang, K.W., D.Y.

Methodology: R.B., E.C., Zhiwei Ding, Zhuokun Ding, A.S.E., P.G.F., R.F., E.F., J.F., T.M., L.N., T.O., C. Papadopoulos, S. Papadopoulos, S. Patel, K.P., J.R., F.H.S., A.S.T., D.T., P.T., E.Y. Walker, E.Y. Wang, K.W., D.Y.

Investigation: Zhiwei Ding, Zhuokun Ding, P.G.F., R.F., E.F., J.F., T.M., L.N., S. Papadopoulos, S. Patel, K.P., J.R., C.S., D.T., P.T., E.Y. Wang

Software: R.B., E.C., Zhiwei Ding, Zhuokun Ding, P.G.F., E.F., J.F., T.O., C. Papadopoulos, S. Papadopoulos, S. Patel, Y.Q., F.H.S., E.Y. Wang, K.W., D.Y.

Resources: P.G.F., R.F., E.F., T.M., L.N., S. Papadopoulos, S. Patel, X.P., K.P., J.R., Z.H.T., A.S.T., D.Y.

Data Curation: Zhiwei Ding, Zhuokun Ding, P.G.F., R.F., E.F., J.F., T.M., L.N., C. Papadopoulos, S. Papadopoulos, S. Patel, K.P., Y.Q., C.S., D.T., P.T., E.Y. Wang, K.W.

Validation: Zhiwei Ding, Zhuokun Ding, P.G.F., R.F., J.F., T.M., L.N., S. Papadopoulos, S. Patel, K.P., Y.Q., J.R., D.T., P.T., E.Y. Wang, K.W.

Supervision: A.S.E., P.G.F., K.F., X.P., J.R., S.S., F.H.S., A.S.T., K.W.

Funding Acquisition: A.S.E., K.F., X.P., J.R., S.S., F.H.S., A.S.T.

Acknowledgements

Data collection, processing, and release efforts spanning 8+ years were supported by a broad set of federal, institutional, and private funders. The work was generously supported by The James Fickel Enigma Project Fund; the Intelligence Advanced Research Projects Activity (IARPA) via the Department of Interior/Interior Business Center (DoI/IBC) under the MICrONS Program (contract numbers D16PC00003, D16PC00004, D16PC0005, and 2017-17032700004); the Defense Advanced Research Projects Agency (DARPA) under Contract No. N66001-19-C-4020; and the National Science Foundation and U.S. Department of Defense OUSD (R&E) under Cooperative Agreement DBI-2229929 (the NSF AI Institute for Artificial and Natural Intelligence). Additional U.S. federal support was provided by the National Science Foundation (NSF) via NeuroNex grant 1707400 and CAREER grant IOS-1552868; the National Institutes of Health (NIH) via National Eye Institute awards R01 EY026927, T32-EY-002520-37 (Core Grant for Vision Research), and F30 EY025510; National Institute of Mental Health and National Institute of Neurological Disorders and Stroke awards U19 MH114830, U01 NS113294, RF1 MH126883, RF1 MH130416, and F30-MH112312. European and German support included the European Research Council (ERC) under the European Union's Horizon Europe research and innovation programme (grant agreements 101041669 and 101171526); the Deutsche Forschungsgemeinschaft (DFG) through SFB 1233 (project 276693517), SFB 1456 (project 432680300), SFB 1528 (project 454648639), project 515774656, and the Cluster of Excellence "Machine Learning – New Perspectives for Science" EXC 2064/1 (project 390727645); the German Federal Ministry of Education and Research (BMBF) via the Collaborative Research in Computational Neuroscience (CRCNS; FKZ 01GQ2107); a ZIM grant via the Federal Ministry for Economic Affairs and Energy (ZF4076506AW9); the Ministry of Science and Culture of Lower Saxony via the zukunft.niedersachsen program of the Volkswagen Foundation for the "CAIMed" project (ZN4257); and the International Max Planck Research School for Intelligent Systems (K.W.). Further institutional and foundation support was provided by the Carl-Zeiss-Stiftung, the Institutional Strategy of the University of Tübingen (DFG ZUK 63), the Baylor College of Medicine Medical Scientist Training Program, and Baylor Research Advocates for Student Scientists (BRASS). Computing resources were provided by the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory (U.S. Department of Energy Contract DE-AC05-00OR22725), the Marlowe supercomputing cluster at Stanford, and the Emmy/Grete supercomputer at NHR-Nord@Göttingen as part of the NHR infrastructure, together with an AWS Machine Learning Research Award and support from NVIDIA. The U.S. Government is authorized to reproduce and distribute reprints for Governmental purposes notwithstanding any copyright annotation thereon. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH, NSF, NEI, NIMH, NINDS, IARPA, DoI/IBC, DARPA, the U.S. Department of Defense, the U.S. Department of Energy, or the U.S. Government.

Data sources and attribution

The experiments in the OmniMouse dataset are aggregated from multiple projects and original sources. Please consult the metadata table to identify the originating project(s) for any experiment you use, and cite the corresponding paper(s) accordingly.

Citation

@dataset{fahey2026omnimouse_data,
  author       = {Fahey, Paul G. and Ponder, Kayla and Muhammad, Taliah and
                  Froebe, Rachel and Ntanavara, Lydia and Tan, Zheng H. and
                  Patel, Saumil and Cobos, Erick and Ding, Zhiwei and
                  Fu, Jiakun and Ding, Zhuokun and Tran, Dat and
                  Papadopoulos, Stelios and Wang, Eric Y. and
                  Turishcheva, Polina and Willeke, Konstantin and
                  Papadopoulos, Christos and Yatsenko, Dimitri and
                  Smith, Cameron and Pierzchlewicz, Pawel A. and
                  Olschewski, Tom and Burghardt, Ren{\'e} and
                  Qiu, Yongrong and Sanborn, Sophia and Pitkow, Xaq and
                  Franke, Katrin and Walker, Edgar Y. and
                  Froudarakis, Emmanouil and Reimer, Jacob and
                  Ecker, Alexander S. and Sinz, Fabian H. and
                  Tolias, Andreas S.},
  title        = {{OmniMouse Two-Photon Calcium Imaging Dataset}},
  year         = {2026},
  publisher    = {Hugging Face},
  doi          = {10.57967/hf/8529},
  url          = {https://huggingface.co/datasets/the-enigma-project/omnimouse-dataset},
  note         = {Companion dataset to Willeke et al., OmniMouse, ICLR 2026}
}