Type: Electrophysiology / Probes,

Type: Optics / Microscopy,

Keywords: Neuropixel recordings, Two-photon imaging, In vivo, Systems neuroscience, Neuronal recordings, Observatory, Mice

A community-driven brain observatory for large-scale systems neuroscience

OpenScope opens the Allen Brain Observatory pipeline to the community, enabling theoretical, computational, and experimental scientists to test sophisticated hypotheses on brain function in a process analogous to astronomical observatories that survey the night sky. Once a year OpenScope will accept experimental proposals from external scientists, which will be reviewed by a panel of leading experts for their feasibility and scientific merit. The Allen Institute will carry out the selected experiments following verified, reproducible, and open protocols for in vivo single- and multi-area two photon calcium imaging and Neuropixels electrophysiology, making the data freely available to these scientists and to the community. This will lower barriers to testing new hypotheses about brain function, bring new computational and theoretical talents into the field, and enhance the reproducibility of results in brain research, thereby accelerating progress toward an integrated understanding of neural activity in health and disease.

* End-to-end standardized experimental platform including brain surgery, animal training, neuronal recordings (in vivo electrophysiology or calcium imaging) and brain reconstruction.

* Data standardization and sharing via NWB files in the cloud.

* Yearly application cycle evaluating scientific proposals from the entire community.

* Behavior animal training to test novel hypothesis of brain function.

* To test an existing hypothesis on brain function at scale with in vivo neuronal recordings.

* To characterize neuronal responses with either two photon calcium imaging (single or multi-plane imaging) or electrophysiological recordings (single or multi-probes recordings).

* Used to study neuronal communication during either passively viewing or behavioral tasks.

* Used to distribute standardized experimental datasets to the community.

* Measuring stimulus-evoked neurophysiological differentiation in distinct populations of neurons in mouse visual cortex (

* Learning from unexpected events in the neocortical microcircuit (

* Parallel inference of hierarchical latent dynamics in two-photon calcium imaging of neuronal populations (

* Mouse / mice

* OpenScope platform tests novel hypotheses on brain function using an established data collection pipeline.

* Platform utilizes cutting- edge Neuropixel recordings, two-photon calcium imaging, and behavioral training.

* Data is curated, standardized, and disseminated with open standards.

* All datasets collected on the platform are cross-referenced through shared standards and data access, allowing further meta-analysis and comparison by the community.

* de Vries, S. E., Lecoq, J. A., Buice, M. A., Groblewski, P. A., Ocker, G. K., Oliver, M., … & Koch, C. (2020). A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex. Nature neuroscience, 23(1), 138-151.

* Siegle, J. H., Jia, X., Durand, S., Gale, S., Bennett, C., Graddis, N., … & Koch, C. (2021). Survey of spiking in the mouse visual system reveals functional hierarchy. Nature, 1-7.


Jerome Lecoq, Principal Scientist


Allen Institute, Seattle, WA



Jerome Lecoq, Christof Koch, Josh Siegle, Sarah Naylor, John Philips, Peter Groblewski, Shawn Olsen, Severine Durand, Tamina Ramirez, Shiella Caldejon, Ali Williford



NIH U24 NS113646-01A1