diff --git a/docs/source/explore_analyze/outreach.md b/docs/source/explore_analyze/outreach.md index 243e7fe..e261a1d 100644 --- a/docs/source/explore_analyze/outreach.md +++ b/docs/source/explore_analyze/outreach.md @@ -1,205 +1,218 @@ # Outreach Events & Resources -This page highlights outreach events organized by our group, including workshops, hackathons, conference sessions, and education activities. It also serves as a hub for associated learning materials such as code tutorials, repositories, and supporting resources. +The Data and Outreach group hosts a number of outreach events to make data, tools, and scientific workflows from the Allen Institute / Neural Dynamics accelerator accessible to the broader community. This page highlights useful resources, such as code tutorials, documentation, and GitHub repos, created for notable events. -Our outreach efforts are designed to make Allen Institute for Neural Dynamics datasets, tools, and scientific workflows more accessible to the broader community. - -You can also view previous and upcoming outreach events here: https://www.allenneuraldynamics.org/events. - ---- -## Types of Outreach Events - -Our outreach efforts span several formats, including: - -- **Workshops** — structured training sessions focused on data, tools, and analysis workflows -- **Hackathons** — collaborative coding events centered on open-ended data exploration and project development -- **Conference sessions** — talks, tutorials, and workshops at scientific meetings -- **Classroom outreach** — course-integrated tutorials and student-facing educational activities - ---- - -## Featured Resources - -This section highlights materials that may be useful beyond the original event they were created for. - -- **Summer Workshop on the Dynamic Brain 2025 collection** - Code Ocean collection for a two-week summer training course, includes code tutorials for multiple projects and datasets. - [View collection](https://codeocean.allenneuraldynamics.org/collections/815cebfe-1829-4287-8e99-f1346b5d6ccb) - -- **Credit Assignment During Learning tutorial** - Code Ocean capsule with code tutorials to access the BCI neurophysiology and behavior dataset. - [View capsule](https://codeocean.allenneuraldynamics.org/capsule/0692322/tree/v3) ---- - -## Workshops - -Workshops provide structured training experiences focused on datasets, tools, and computational approaches used across the Allen Institute for Neural Dynamics. - -### Summer Workshop on the Dynamic Brain 2025 - -**Date:** August 24 – September 7, 2025 -**Audience:** graduate students, researchers -**Location:** Friday Harbor Laboratories, San Juan Island, WA, USA -**Highlighted projects/platforms:** multiple Allen Institute large-scale neural datasets - -A two-week summer course focused on computational analysis of large-scale neuroscience datasets. - -#### Resources -- [Code Ocean collection](https://codeocean.allenneuraldynamics.org/collections/815cebfe-1829-4287-8e99-f1346b5d6ccb) -- [SWDB Data Book](https://allenswdb.github.io/intro.html) +Browse by project and platform to see specific events and their associated resources. Feel free to reuse any of these materials for your work. --- -### Workshop at Western Washington University - -**Date:** October 30, 2025 - -**Audience:** undergraduate students, graduate students (neuroscience, biology, computer science) -**Location:** WWU, Bellingham, WA, USA -**Highlighted projects/platforms:** Brain-wide Anatomy, Exa-SPIM, Credit Assignment During Learning +To view a list of previous and upcoming outreach events, check out the [Neural Dynamics events page](https://www.allenneuraldynamics.org/events). -This workshop included short talks on team science, an overview of Allen Institute for Neural Dynamics, and hands-on code tutorials using neuron reconstructions from the Brain-wide Anatomy platform and neurophysiology and behavior data from the BCI project. - -#### Resources -- [Exa-SPIM tutorial capsule](https://codeocean.allenneuraldynamics.org/capsule/0685965/tree/v1) -- [BCI / Credit Assignment tutorial capsule](https://codeocean.allenneuraldynamics.org/capsule/0692322/tree/v1) +Browse the full library of [publicly available Code Ocean capsules](https://codeocean.allenneuraldynamics.org/collections/4a2d5da6-b053-43fe-9180-1912d787c59e?page=1&filter=all&refine=public). --- -### Workshop at Okinawa Institute of Science and Technology +## Outreach Resources Organized by Project and Platform -**Date:** January 30, 2025 -**Audience:** researchers -**Location:** OIST, Okinawa, JP -**Highlighted projects/platforms:** Brain-wide Anatomy, Electrophysiology +### Dynamic Routing +*Project* -This workshop focused on introducing and sharing resources from the Brain-wide Anatomy and Electrophysology platforms. +This project studies task-switching behaviors in mice to determine how neuronal circuits are reconfigured to dynamically route information for different tasks. +**Resources** ---- +- [Project Page](https://www.allenneuraldynamics.org/projects/dynamic-routing) -## Hackathons +- [Dynamic Routing code tutorial](https://codeocean.allenneuraldynamics.org/capsule/0831127/tree/v3) — Code Ocean public collection with code tutorials on how to access the electrophysiology and behavior datasets. -Hackathons are collaborative coding events where participants work directly with Allen Institute datasets and develop exploratory analyses, tools, or prototype research workflows. +**Events featuring this project** -### University of Washington Neurohackathon (2026) +> **UW CNC–AIND Hackacollabathon: Dynamic Routing** +> +> - **Date:** May 20, 2026 +> - **Audience:** Graduate students, postdocs, researchers +> - **Location:** UW, Seattle, WA +> +> A collaborative hackathon to share new data from the project with researchers at UW and the Allen Institute. -**Date:** March 6–8, 2026 -**Audience:** undergraduate students, graduate students, researchers -**Location:** UW, Seattle, WA, USA -**Highlighted projects/platforms:** Credit Assignment During Learning +> **Summer Workshop on the Dynamic Brain 2026** +> +> - **Date:** Aug 23 – Sept 6, 2026 +> - **Audience:** Graduate students, postdocs +> - **Location:** Friday Harbor, WA +> +> A project-based, residential summer course where students learn computational methods for analyzing large-scale neuroscience data. +> +> Resource: [Behavior States and Neuronal Decoding Tutorial](https://codeocean.allenneuraldynamics.org/capsule/2687719/tree/v2) -Our second year participating in the UW Neurohackathon, sharing updated data and tutorials from the *Credit Assignment During Learning* project. - -#### Resources -- [BCI / Credit Assignment tutorial capsule](https://codeocean.allenneuraldynamics.org/capsule/0692322/tree/v3) +> **Undergraduate Course at University of Puget Sound** +> +> - **Date:** Sept 23, 2026 +> - **Audience:** Undergraduate students +> - **Location:** UPS, Tacoma, WA +> +> Lecture for a class where students developed semester-long research projects using Allen Institute datasets. +> +> Resource: [Course Materials](https://github.com/leesuyee/dynamic-routing-tutorials) --- -### University of Washington Neurohackathon (2025) - -**Date:** May 16–18, 2025 -**Audience:** undergraduate students, graduate students, researchers -**Location:** UW, Seattle, WA, USA -**Highlighted projects/platforms:** Credit Assignment During Learning - -A hackathon organized by the Conect and Synaptech student clubs at UW, where participants used neurotechnology devices and/or Allen Institute neural datasets to develop a project or prototype. - -#### Resources -- [BCI / Credit Assignment tutorial capsule](https://codeocean.allenneuraldynamics.org/capsule/6784496/tree/v1) +### Credit Assignment During Learning +*Project* + +This project uses a brain-computer interface (BCI) learning task coupled with an optical connection-mapping technique to investigate how the brain updates synaptic connections to support learning. + +**Resources** + +- [Project Page](https://www.allenneuraldynamics.org/projects/credit-assignment-during-learning) + +- [Credit Assignment During Learning code tutorial](https://codeocean.allenneuraldynamics.org/capsule/4369277/tree/v4) — Code Ocean public collection with code tutorials on how to access the neurophysiology and behavior datasets. + +**Events featuring this project** + +> **UW CNC–AIND Hackacollabathon: Credit Assignment During Learning** +> +> - **Date:** May 14, 2025 +> - **Audience:** Graduate students, postdocs, researchers +> - **Location:** UW, Seattle, WA +> +> A collaborative hackathon to share new data from the project with researchers at UW and the Allen Institute. + +> **University of Washington Neurohackathon (2025, 2026)** +> +> - **Dates:** May 16–18, 2025 and Mar 6–8, 2026 +> - **Audience:** Undergraduate students, graduate students, researchers +> - **Location:** UW, Seattle, WA +> +> A long-standing hackathon hosted by the CoNECT and Synaptech student clubs where participants used neurotechnology devices and/or Allen Institute neural datasets to build a project. + +> **Undergraduate Course at University of Puget Sound** +> +> - **Date:** Sept 24, 2025 +> - **Audience:** Undergraduate students +> - **Location:** UPS, Tacoma, WA +> +> Lecture for a class where students developed semester-long research projects using Allen Institute datasets. +> +> Resource: [Course Materials](https://github.com/AllenNeuralDynamics/ups_nrsc490_tutorial/tree/main) + +> **Workshop at Western Washington University** +> +> - **Date:** Oct 30, 2025 +> - **Audience:** Undergraduate students, graduate students +> - **Location:** WWU, Bellingham, WA +> +> A workshop introducing the Allen Institute / Neural Dynamics accelerator to the research community at WWU, featuring talks from WWU alumni now at the Allen Institute, an overview of the group's projects, platforms, and approach to science, and hands-on code tutorials using Exa-SPIM and BCI data. +> +> Resource: [Code Tutorial](https://codeocean.allenneuraldynamics.org/capsule/0692322/tree/v3) --- -### UW CNC–AIND Hackacollabathon: Credit Assignment During Learning +### Neural Dynamics in Multi-Regional Circuits with Thalamus in the Middle +*Project* -**Date:** May 14, 2025 -**Audience:** graduate students, researchers -**Location:** UW,Seattle, WA, USA -**Highlighted projects/platforms:** Credit Assignment During Learning +This project investigates how neural signals are transmitted from subcortical brain regions via the thalamus to modulate cortical activity and influence behavior. -A collaborative hackathon to share new data from the *Credit Assignment During Learning* project with researchers at UW and the Allen Institute. +**Resources** -#### Resources -- [BCI / Credit Assignment tutorial capsule](https://codeocean.allenneuraldynamics.org/capsule/6784496/tree/v1) +- [Project Page](https://www.allenneuraldynamics.org/projects/neural-dynamics-in-multi-regional-circuits-with-thalamus-in-the-middle) ---- - -### UW CNC–AIND Hackacollabathon: Mesoscale Connectivity +- [Mesoscale Connectivity tutorial capsule](https://codeocean.allenneuraldynamics.org/capsule/6784496/tree/v1) — Code Ocean public collection with code tutorials on how to access the anatomy data. -**Date:** December 4, 2024 -**Audience:** undergraduate students, graduate students, researchers -**Location:** UW, Seattle, WA, USA -**Highlighted projects/platforms:** Thalamus in the Middle, Brain-wide Anatomy +**Events featuring this project** -A collaborative hackathon to share new data from the *Thalamus in the Middle* project with researchers at UW and the Allen Institute. +> **UW CNC–AIND Hackacollabathon: Mesoscale Connectivity** +> +> - **Date:** Dec 4, 2024 +> - **Audience:** Undergraduate students, graduate students, postdocs, researchers +> - **Location:** UW, Seattle, WA +> +> A collaborative hackathon to share new data from this project with researchers at UW and the Allen Institute. -#### Resources -- [Mesoscale Connectivity tutorial capsule](https://codeocean.allenneuraldynamics.org/capsule/6784496/tree/v1) +> **Code Tutorial for High School Field Trip** +> +> - **Date:** Feb 13, 2026 +> - **Audience:** High school students +> - **Location:** Allen Institute, Seattle, WA +> +> Introduced neural anatomy data and how to map connections between brain areas for high school students visiting the Institute. +> +> Resource: [Code Tutorial Repository](https://github.com/leesuyee/mesoscale-connectivity-tutorial) --- -## Conference Sessions & Talks +### Brain-Wide Anatomy at Synaptic Resolution +*Platform* -Conference sessions and invited talks help introduce Allen Institute datasets, tools, and scientific resources to broader technical and research communities. +Combines innovative histology, ExA-SPIM microscopy, image processing, and machine learning to map the morphology of individual neurons across the whole brain at high throughput. -### Talk at Cosyne Tutorial Session +**Resources** -**Date:** March 12, 2026 -**Audience:** researchers -**Location:** Cosyne, Lisbon, PT -**Highlighted projects/platforms:** Brain-wide Anatomy, Electrophysiology, AIND Community Portal, Dynamic Routing, Visual Behavior Neuropixels +- [Platform Page](https://www.allenneuraldynamics.org/platforms/brain-wide-anatomy-at-cellular-resolution) -A talk delivered during the Cosyne tutorial session highlighting datasets, tools, and resources from the Allen Institute for Neural Dynamics. +- [Exa-SPIM tutorial capsule](https://codeocean.allenneuraldynamics.org/capsule/5871121/tree/v1) — Code Ocean public collection with code tutorials on how to access the morphology dataset. ---- +**Events featuring this platform** -### Talk at the NeurIPS Data on the Brain & Mind Workshop +> **UW CNC–AIND Hackacollabathon: ExaSPIM** +> +> - **Date:** Dec 6, 2023 +> - **Audience:** Undergraduate students, graduate students, postdocs, researchers +> - **Location:** UW, Seattle, WA +> +> A collaborative hackathon to share new data from this project with researchers at UW and the Allen Institute. -**Date:** December 7, 2025 -**Audience:** researchers (machine learning, AI, neuroscience) -**Location:** NeurIPS 2025, San Diego, CA, USA -**Highlighted projects/platforms:** Visual Behavior Neuropixels +> **Workshop at Western Washington University** +> +> - **Date:** Oct 30, 2025 +> - **Audience:** Undergraduate students, graduate students +> - **Location:** WWU, Bellingham, WA +> +> A workshop introducing the Allen Institute / Neural Dynamics accelerator to the research community at WWU, featuring talks from WWU alumni now at the Allen Institute, an overview of the group's projects, platforms, and approach to science, and hands-on code tutorials using Exa-SPIM and BCI data. +> +> Resource: [Code Tutorial](https://codeocean.allenneuraldynamics.org/capsule/0685965/tree/v1) -A short talk during a workshop on AI applications for neuroscience and cognitive science data, highlighting a preprint and code tutorial from the Visual Behavior Neuropixels project. -#### Resources -- [Workshop website](https://data-brain-mind.github.io/) -- [Blogpost on the tutorial](https://data-brain-mind.github.io/tutorials/an-overview-of-the-neuropixels-visual-behavior-dataset-from-the-allen-institute/) +> **Talk at Cosyne Tutorial Session** +> +> - **Date:** Mar 12, 2026 +> - **Audience:** Researchers +> - **Location:** Cosyne, Lisbon, PT +> +> Talk highlighting datasets, tools, and resources from Neural Dynamics, sharing recent developments across projects and platforms. --- -### Lectures & Classroom Outreach - -Lectures and classroom activities support student learning by introducing Allen Institute datasets and computational neuroscience workflows in educational settings. +### Multi-Neuropixels Electrophysiology +*Platform* -### Lecture at Undergraduate Course at University of Puget Sound +Implements pioneering technology to support highly reproducible, targeted, brain-wide electrophysiology. -**Date:** September 24, 2025 -**Audience:** undergraduate students (neuroscience, computer science) -**Location:** UPS, Tacoma, WA, USA -**Highlighted projects/platforms:** Credit Assignment During Learning - -A lecture for an undergraduate class in which students developed quarter-long research projects using Allen Institute datasets. - -#### Resources -- [Code tutorial repository](https://github.com/AllenNeuralDynamics/ups_nrsc490_tutorial/tree/main) - ---- +**Resources** -### Code Tutorial for High School Field Trip +- [Platform Page](https://www.allenneuraldynamics.org/platforms/neuropixels-electrophysiology) +- [Ephys NWB Tutorial Capsule](https://codeocean.allenneuraldynamics.org/capsule/0691868/tree/v1) — Code Ocean public collection with code tutorials on how to access the electrophysiology dataset. -**Date:** February 13, 2026 -**Audience:** high school students -**Location:** Allen Institute, Seattle, WA, USA -**Highlighted projects/platforms:** Thalamus in the Middle, Brain-wide Anatomy +**Events featuring this platform** -A code tutorial for high school group visiting the Allen Institute, focused on introducing neural anatomy data and mapping connections between brain areas. +> **UW CNC–AIND Hackacollabathon: Ephys** +> +> - **Date:** Jan 18, 2023 +> - **Audience:** Undergraduate students, graduate students, postdocs, researchers +> - **Location:** UW, Seattle, WA +> +> A collaborative hackathon to share new data from this project with researchers at UW and the Allen Institute. -#### Resources -- [Code tutorial repository](https://github.com/leesuyee/mesoscale-connectivity-tutorial) +> **Talk at Cosyne Tutorial Session** +> +> - **Date:** Mar 12, 2026 +> - **Audience:** Researchers +> - **Location:** Cosyne, Lisbon, PT +> +> Talk highlighting datasets, tools, and resources from the Institute, sharing recent developments across projects and platforms. --- -### Have questions? Interested in using our materials? +## Have questions? -Contact the Data & Outreach team. \ No newline at end of file +Contact the Data & Outreach team. \ No newline at end of file