Capsule with notebooks demonstrating PyNWB data access along with exercises and problem sets to practice data access patterns and learn about additional datasets.
Objectives
In this workshop, we will briefly introduce the datasets made available for SWDB, walking through how to load, find, and access the data and metadata. After working through the material, you will learn:
- how to use AllenSDK and pynwb to load and access data stored in Neurodata Without Borders (NWB) files
- how to use the metadata and the SWDB Data Book to find more information about the datasets
Data Access: AllenSDK and pynwb
The SWDB datasets are packaged as NWB files, a standardized data format for neurophysiology data. We'll show you 2 Python toolkits for accessing NWB files: PyNWB and AllenSDK. PyNWB is the official API for NWB files while the AllenSDK is a Python package developed for accessing Allen Brain Atlas data (including the Brain Observatory datasets). This workshop is split into 2 Code Ocean capsules with the corresponding environment setup and attached datasets for each toolkit. You can use these capsules as templates for your own work, depending on the dataset you choose to work with. This capsule is focused on PyNWB access.
Notebooks include:
- Workshop-2-Data-Access-pynwb.ipynb
- Workshop-2-SciQuest-Learning.ipynb
GitHub repo for this capsule: https://github.com/AllenSWDB/SWDB_2025_DataIntro
GitHub repo for SWDB 2025: https://github.com/AllenInstitute/swdb_2025_student/wiki
Acknowledgments to contributors: Suyee Lee, Marina Garrett, Saskia de Vries, Kayvon Daie, Andrew Shelton