OpenScope: A platform for high-throughput and reproducible neurophysiology open to external scientists to test theories of brain function
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 from the international community for their feasibility and scientific merit. The Allen Institute will carry out the selected in vivo experiments in mice brains 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.
2022 Letter of Intent Due Date: Sept. 12, 2022
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 global scientific community.
Animal behavior training to test novel hypotheses of brain function.
New research to understand how the brain handles optical illusions and makes predictions
May 9, 2022
3 new projects launch on OpenScope, a shared neuroscience observatory
A day in the (neuroscience) life: OpenScope
March 18, 2022
Scientists on the OpenScope team help share the Allen Institute’s ‘observatory of the mind’ with the larger scientific community
Three collaborative studies launch on ‘OpenScope,’ a shared observatory for neuroscience
September 24, 2019
2019 projects will tackle Alzheimer’s disease, motion detection, and how the brain processes contextual information
- 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.
- Experimental data is eventually released to the public after a minimum one year embargo.
All datasets collected on the platform are cross-referenced through shared standards and data access, allowing further meta-analysis and comparison by the community. An external team will need to analyze and then submit the outcome to bioRxiv and a journal. We don’t own the data, which will have restricted access for a one year period.
Possible scientific applications:
- 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.
Example use (previously funded projects):
- 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
Access to the OpenScope program is available to scientists internationally. All experimental work is generously supported by an NIH U24 resource grant (U24 NS113646-01A1) to serve the global scientific community. The Allen Brain Observatory platform was initiated and established in 2016 thanks to funding from Paul G. Allen and the Falconwood Foundation.
Application and selection process:
- Two-stage selection process: Short letters of intent are first selected for a full application submission.
- Double-blinded scientific review.
- Letter of Intent Due: September 12, 2022
- Full Proposal Due: November 7, 2022