Vision
OpenScope provides access to cutting-edge neurophysiological methods to scientists across the world. Similar to astronomical observatories, scientists propose experiments that are then executed at the Allen Institute. All data is made openly available using modern data science pipelines and standardized formats.
- Record from thousands of neurons across the mouse brain using either multi-probes Neuropixels recordings or multi-area two photon calcium imaging.
- An end-to-end standardized experimental platform including brain surgery, animal behavioral training, neuronal recordings and brain reconstruction.
- All datasets are shared as standardized Neurodata Without Borders (NWB) files in a public archive (DANDI) in the cloud.
- A double-blinded yearly application cycle evaluating scientific proposals from the global scientific community.
Learn More
Submit A Project
Once a year, OpenScope accepts experimental proposals from external scientists following a Request for Proposals (RFP, OpenScope_RFP_2024-2025). Application details for the OpenScope program can be found here: How to Apply to the OpenScope Program.
Advantages
- The OpenScope platform tests novel hypotheses on brain function using an already established data collection pipeline, potentially accelerating your science.
- You directly leverage the experience of the Allen Institute teams for your project and scientific questions.
- Data is curated, standardized and disseminated with open standards, you can focus on pushing data analysis.
- During the one year embargo period, the application team analyzes the data and leads publication of scientific results with guaranteed first and last authorships.
- Experimental data is eventually released to the public after a minimum one year embargo from when data collection ends. This can further the impact of your work and lead to additional collaborations and data publications.
- All datasets collected on the platform are cross-referenced through shared standards and data access, allowing further meta-analysis and comparison by the community.
- Data sharing is facilitated through the OpenScope Data Portal. This portal is designed to facilitate collaborations.
- All project can directly leverage a growing ecosystem of pre-written analysis routines in the cloud, available through the OpenScope Databook. This includes advanced dimensionality reduction analysis like CEBRA as well as basic analysis like stimuli responses analysis.
Scientific publications associated with OpenScope projects
All projects executed by the OpenScope projects aim to be released first as bioRxiv publication and eventually in a reviewed journal. The application team is empowered to lead this publication and control authorship of these pieces (both first and last-authors).
- Mayner, W. G. P. et al. Measuring Stimulus-Evoked Neurophysiological Differentiation in Distinct Populations of Neurons in Mouse Visual Cortex. eNeuro 9, (2022)
- Prince, L. Y., Bakhtiari, S., Gillon, C. J. & Richards, B. A. Parallel inference of hierarchical latent dynamics in two-photon calcium imaging of neuronal populations. bioRxiv 2021.03.05.434105 (2021)
- Gillon, C. J. et al. Learning from unexpected events in the neocortical microcircuit. bioRxiv 2021.01.15.426915 (2023)
- Gillon, C. J. et al. Responses of pyramidal cell somata and apical dendrites in mouse visual cortex over multiple days. Sci Data 10, 287 (2023)
- Wyrick, D. G. et al. Differential encoding of temporal context and expectation under representational drift across hierarchically connected areas. bioRxiv 2023.06.02.543483 (2023)
- Shin, H. et al. Recurrent pattern completion drives the neocortical representation of sensory inference. bioRxiv 2023.06.05.543698 (2023)
Published Datasets on DANDI Archive
You can access the OpenScope Data Portal for newer projects metadata information, experimental design descriptions, analysis notebooks and more. All projects conducted by the OpenScope program are released on Dandi Archive. We also provide a comprehensive set of data introductory notebooks in the OpenScope Databook.
Funding
Access to the OpenScope program is available to scientists internationally for free. 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 The Paul G. Allen Family Foundation and the Falconwood Foundation.
Published annual reports
The OpenScope program publishes on an annual basis a detailed public report that summarizes all of our activities within the year. These reports highlight all developments of the year: new selected projects, completed projects, publications and technical developments of the platform.
Contact
We are available to answer any question! Please do not hesitate to reach out via openscope@alleninstitute.org. Drafting a project for our platform is a collaborative process.
