How to read NWB files (incl. streaming)
NWBStreaming
Past installment · NeuroDataReHack
NeuroDataReHack 2025
Generate new insights from existing neurophysiology data through secondary analysis.
- Dates
- July 14–18, 2025 · arrive Sunday, July 13
- Venue
- HHMI Janelia Research Campus, Ashburn, Virginia, United States
- Organizers
- Ben Dichter, Stephanie Prince, Ryan Ly, Oliver Rübel
24
participants
21
institutions
8
countries
10
projects
15
recordings
About this year
NeuroDataReHack 2025 brought 24 participants from 21 institutions in eight countries to Janelia for five days. This year had more collaborative projects than previous years, with several teams of four to six people working on larger, more ambitious questions and participants naturally adopting roles of teachers and students within their groups.
Following the event, participants were invited to apply for a Kavli Foundation Neurodata Discovery Award, which provides funding to continue data reanalysis projects begun at the workshop.
Instructors
Lawrence Berkeley National Laboratory
Lawrence Berkeley National Laboratory
Flatiron Institute
HHMI Janelia Research Campus
University of Edinburgh
Flatiron Institute
Allen Institute for Neural Dynamics
International Brain Laboratory
HHMI Janelia Research Campus
HHMI Janelia Research Campus
HHMI Janelia Research Campus
Schedule
Two talks (the welcome and the overview of NWB and DANDI) were not recorded because of a technical issue.
The welcome talk and the overview of NWB and DANDI were not recorded because of a technical issue.
Day 0Sunday, July 13Arrival
| Time | Session | Speaker |
|---|---|---|
| 7:00 PM – 8:30 PM | Arrival and dinner |
Day 1Monday, July 14Accessing data and starting projects
| Time | Session | Speaker |
|---|---|---|
| 8:00 AM – 9:00 AM | Breakfast | |
| 9:00 AM – 9:30 AM | Welcome to NeuroDataReHack 2025 (not recorded) | Ben DichterCatalystNeuro |
| 9:30 AM – 10:30 AM | Introduction to NWB and DANDI (not recorded) | Ryan LyLawrence Berkeley National Laboratory |
| 10:30 AM – 11:30 AM | How to read NWB files (incl. streaming) | Stephanie PrinceLawrence Berkeley National Laboratory |
| 11:30 AM – 12:00 PM | A tour of NWB Dandisets & searching tools | Ben DichterCatalystNeuro |
| 12:00 PM – 12:30 PM | Data from The International Brain Lab | Mayo FaulknerInternational Brain Laboratory |
| 12:30 PM – 1:30 PM | Lunch | |
| 1:30 PM – 2:15 PM | Introduction to OpenScope and DataBook | Carter PeeneAllen Institute for Neural Dynamics |
| 2:15 PM – 3:45 PM | Project roundtable | Ryan LyLawrence Berkeley National Laboratory |
| 3:45 PM – 5:30 PM | Hacking on projects | |
| 5:30 PM – 6:30 PM | Speed networking | Ben DichterCatalystNeuro |
| 6:30 PM – 7:30 PM | Dinner |
Day 2Tuesday, July 15Analyzing data
| Time | Session | Speaker |
|---|---|---|
| 8:00 AM – 9:00 AM | Breakfast | |
| 9:00 AM – 9:15 AM | Introduction to Day 2 | Ben DichterCatalystNeuro |
| 9:15 AM – 10:00 AM | SpikeInterface | Chris HalcrowUniversity of Edinburgh |
| 10:00 AM – 10:45 AM | Neural Data Analysis with Pynapple | Guillaume ViejoFlatiron Institute |
| 10:45 AM – 11:30 AM | OpenScope DataBook (electrophysiology) | Carter PeeneAllen Institute for Neural Dynamics |
| 11:30 AM – 12:30 PM | Hacking on projects | |
| 12:30 PM – 1:30 PM | Lunch | |
| 1:30 PM – 2:00 PM | Dandiset showcase: Glia Accumulate Evidence that Actions Are Futile and Suppress Unsuccessful Behavior | Misha AhrensHHMI Janelia Research Campus |
| 2:00 PM – 2:45 PM | OpenScope DataBook (calcium imaging) | Carter PeeneAllen Institute for Neural Dynamics |
| 2:45 PM – 3:15 PM | Spyglass | Alison ComrieUniversity of California, San Francisco |
| 3:15 PM – 3:30 PM | Refreshments break | |
| 3:30 PM – 4:30 PM | Neurosift visualizations and AI chat | Jeremy MaglandFlatiron Institute |
| 4:30 PM – 5:00 PM | Contributing to open source: repos, issues, and pull requests | Ben DichterCatalystNeuro |
| 5:00 PM – 6:30 PM | Hacking on projects | |
| 6:30 PM – 7:30 PM | Dinner |
Day 3Wednesday, July 16Advanced analysis
| Time | Session | Speaker |
|---|---|---|
| 8:00 AM – 9:00 AM | Breakfast | |
| 9:00 AM – 9:10 AM | Introduction to Day 3 | Ben DichterCatalystNeuro |
| 9:10 AM – 9:25 AM | Project check-ins | |
| 9:25 AM – 10:25 AM | Intro to coding with LLMs | Ben DichterCatalystNeuro |
| 10:25 AM – 12:30 PM | Hacking on projects | |
| 12:30 PM – 1:30 PM | Lunch | |
| 1:30 PM – 2:10 PM | Virtual datasets and LINDI | Ben Dichter, Ryan LyCatalystNeuro; Lawrence Berkeley National Laboratory |
| 2:10 PM – 3:30 PM | Hacking on projects | |
| 3:30 PM – 3:45 PM | Group photo | |
| 3:45 PM – 6:30 PM | Hacking on projects | |
| 6:30 PM – 7:30 PM | Dinner |
Day 4Thursday, July 17Hacking on projects
| Time | Session | Speaker |
|---|---|---|
| 8:00 AM – 9:00 AM | Breakfast | |
| 9:00 AM – 9:10 AM | Introduction to Day 4 | Ben DichterCatalystNeuro |
| 9:10 AM – 9:30 AM | Project check-ins | |
| 9:30 AM – 10:00 AM | Converting data to NWB | Ryan LyLawrence Berkeley National Laboratory |
| 10:00 AM – 12:30 PM | Hacking on projects | |
| 12:30 PM – 1:30 PM | Lunch | |
| 1:30 PM – 2:00 PM | Lab tour | Jakob VoigtsHHMI Janelia Research Campus |
| 2:00 PM – 3:30 PM | Hacking on projects | |
| 3:30 PM – 3:45 PM | Refreshments break | |
| 3:45 PM – 6:30 PM | Hacking on projects | |
| 6:30 PM – 7:30 PM | Dinner |
Day 5Friday, July 18Presentations
| Time | Session | Speaker |
|---|---|---|
| 8:00 AM – 9:00 AM | Breakfast | |
| 9:00 AM – 9:10 AM | Introduction to Day 5 | Ben DichterCatalystNeuro |
| 9:10 AM – 10:10 AM | suite2p, rastermap, facemap, cellpose | Carsen StringerHHMI Janelia Research Campus |
| 10:10 AM – 12:30 PM | Hacking on projects | |
| 12:30 PM – 1:30 PM | Lunch | |
| 1:30 PM – 3:30 PM | Project presentations | |
| 3:30 PM – 3:45 PM | Refreshments break | |
| 3:45 PM – 5:15 PM | Project presentations | |
| 5:15 PM – 6:30 PM | Discussion and feedback | |
| 6:30 PM – 7:30 PM | Dinner |
Recordings
Data from The International Brain Lab
IBLElectrophysiology
SpikeInterface
Spike sortingElectrophysiology
OpenScope DataBook (electrophysiology)
OpenScopeElectrophysiology
OpenScope DataBook (calcium imaging)
OpenScopeCalcium imaging
Neurosift visualizations and AI chat
NeurosiftLLMs
Virtual datasets and LINDI
StreamingNWB
Converting data to NWB
Conversion
suite2p, rastermap, facemap, cellpose
Calcium imagingBehavior
Projects
A neurocentric account for context-dependent neural geometry
Zilu Liang, Mia Whitefield, Sumedha Nalluru
One of the core pursuits in neuroscience is to understand how information is encoded in neural activity.
Apply electrophysiological-based neuron classification methods to other dandisets
Stephanie Prince, Ambarish Ghatpande
Several approaches have been recently introduced to classify neurons by cell type based on electrophysiological data; we apply them to a new dandiset to test generalization across datasets.
Cyclic Adversarial Transformers for Temporally Stable Brain Computer Interface Decoding
Lyn Ackert-Smith
Creating robust BCIs is a challenge due to changing populations of neurons, but leveraging stable population dynamics can counteract this effect.
Generating Synthetic MRI Data Using GenAI Models to Enhance Neuroimaging Analyses
Reihaneh Hassanzadeh
This project utilizes generative AI to expand and enrich structural MRI datasets using a diffusion-based model.
Improving Low-Dimensional Embedding of Two-Photon Calcium Imaging Data Using Inferred Spiking Activity
Peter Hogg
Embedding tools like CEBRA can uncover low-dimensional representations of population activity that reflect task or stimulus related neural dynamics.
Mapping the brain across regions with single-unit activity
Cornelius Bergmann, Chris Halcrow, Mayo Faulkner, Ji Xia, Nisrine Bakri, Pierre Le Merre
In this project, we approached the organization of the brain at the level of single neuron activity.
Olfactory Representation in the Piriform Cortex
Nisrine Bakri
Understanding how odors are represented at the single-cell and population levels in the piriform cortex is key to deciphering olfactory perception.
Place field and oscillation changes with mouse kinematics
Yang-Sun Hwang, Eryn Sale
The hippocampus plays a critical role in spatial navigation and memory, but its representations are shaped by more than just the animal's location.
The relationship between neuromodulation and neurovascular coupling
Yunmiao Wang
This project explored spatiotemporal patterns in neurovascular data inspired by research on impulse response functions during spontaneous brain activity.
Whole-brain neuron-astrocyte information flow supporting futility-induced passivity
Marco Celotto, David Makoko, Camille Donoho, Ameyaltzin Castillo Almazán, Koray Cârsteanu, Cheng-Yu Huang
Mu et al. (2019) showed that norepinephrine-astrocyte signaling modulates neuronal activity to mediate futility-induced passivity in zebrafish.
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