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.
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.
Letter of Intent Due: September 22nd, 2021 (5 pm Pacific)
Full Proposal Due: November 22nd, 2021 (5 pm Pacific)
Join us on September 13 for the OpenScope Applicant Webinar to be introduced to the OpenScope resource, meet the OpenScope program team, and learn about the application process, expectations, and recent selected projects. This webinar is open to scientists applying in the 2021 RFP, as well as to those interested in applying in future years. For current applicants, register by September 7 to also access individual consultations with OpenScope staff to discuss your application.
- 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 free to all scientists world-wide. 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:
- Application is open to all scientists world-wide.
- 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 22nd, 2021 (5 pm Pacific)
- Full Proposal Due: November 22nd, 2021 (5 pm Pacific)
Does the bibliography count towards the page limit for the LOI and full proposal?
No, the bibliography may be in addition to the 2pg limit for the LOI and the 6pg limit for the full proposal. However, any other content (including figures) must be within the page limit.
Do I need to be at a certain career stage or have an established lab to apply?
No, this opportunity is open to all scientists worldwide, irrespective of your career level or status. We are ranking proposals on the proposed science and not the team. However, you need to demonstrate that you have a well-informed data analysis plan and the time or commitment to execute that plan.
Are you accepting proposals that involve shipping mice to or from the Allen Institute before or after the data collection?
For this year’s RFP, we are not accepting proposals that involve animals shipped to the Allen Institute (however, we may consider this for future years). We may, however, consider applications that request shipping the animals or samples back to the awardee after the data collection, with the understanding that the awardee would have to complete any histology.
Are you accepting proposals that involves anesthesia, such as isoflurane?
We will consider LOIs involving isoflurane but acceptance of such proposals will depend on the details of the methodology. As there is additional setup and uncertainty with including isoflurane at this time, we suggest you have a strong scientific rationale for including these methods in your proposal.
Are you accepting proposals that involve visual deprivation?
We will consider LOIs involving visual deprivation, but acceptance of such proposals will depend on the details of the methodology and additional conversations and approval with IACUC. As there is additional setup and uncertainty with including visual deprivation at this time, we suggest you have a strong scientific rationale for including these methods in your proposal.
Are you accepting proposals that involve pharmacological manipulation?
No, not for this year.
Are you accepting proposals involving viral manipulations?
No, not for this year.
Are you accepting proposals involving recordings from sleeping animals?
No, not for this year.