The Neurodata Without Borders ecosystem for neurophysiological data science
- Scientific Data Division, Lawrence Berkeley National Laboratory, United States
- Applied Mathematics and Computational Research Division, Lawrence Berkeley National Laboratory, United States
- CatalystNeuro, United States
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, United States
- Department of Otolaryngology - Head and Neck Surgery, Harvard Medical School, United States
- MBF Bioscience, United States
- Allen Institute for Brain Science, United States
- Department of Neurosurgery, Stanford University, United States
- Janelia Research Campus, Howard Hughes Medical Institute, United States
- Kavli Institute for Fundamental Neuroscience, United States
- Departments of Physiology and Psychiatry University of California, San Francisco, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, United States
- Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience, University of California, Berkeley, United States
- Weill Neurohub, United States
Figures
Figure 1
NWB addresses the massive diversity of neurophysiology data and metadata.
(a) Diversity of experimental systems: species and tasks: (i) mice performing a visual discrimination task; (ii) rats performing a memory-guided navigation task; (iii) humans speaking …
Figure 2
NWB enables unified description and storage of multimodal raw and processed data.
(a) Example pipelines for extracellular electrophysiology and optical physiology demonstrate how NWB facilitates data processing. For extracellular electrophysiology (top), raw acquired data is …
Figure 3
The NWB software architecture modularizes and integrates all components of a data language.
(a) Illustration of the main components of the NWB software stack consisting of: (i) the specification language (light blue) to describe data standards, (ii) the data standard schema (lilac), which …
Figure 4
NWB enables creation and sharing of extensions to incorporate new use cases.
(a) Schematic of the process of creating a new neurodata extension (NDX), sharing it, and integrating it with the core NWB data standard. Users first identify the need for a new data type, such as …
Figure 5
NWB is foundational for the DANDI data repository to enable collaborative data sharing.
The DANDI project makes data and software for cellular neurophysiology FAIR. DANDI stores electrical and optical cellular neurophysiology recordings and associated MRI and/or optical imaging data. …
Figure 6
NWB is integrated with state-of-the-art analysis tools throughout the data life cycle.
NWB technologies are at the heart of the neurodata lifecycle and applications. Data standards are a critical conduit that facilitate the flow of data throughout the data lifecycle and integration of …
Figure 7
NWB together with DANDI provides an accessible approach for FAIR sharing of neurophysiology data.
The table above assesses various approaches for sharing neurophysiology data with regard to their compliance with FAIR data principles. Here, cells shown in gray/green indicate non-compliance and …
Figure 8
Coordinated community engagement, governance, and development of NWB.
(a) NWB is open source with all software and documents available online via GitHub and the nwb.org website. NWB provides a broad range of online community resources, e.g., Slack, online Help Desk, …
Appendix 1—figure 1
Visualization of the stimulus (bottom) and response (top) signals recorded via intracellular electrophysiology and stored in NWB.
Appendix 1—figure 2
Visualization of the intracellular electrophysiology file using NWBWidgets.
Appendix 2—figure 1
Files and folders generated by the cookiecutter ndx-template.
The main folder contains the license and readme file for extension along with files required for installing the extension (e.g., setup.py, setup.cfg, MANIFEST.in, and requirements.txt) as well a …
Appendix 3—figure 1
Illustration of the process for creating, publishing, and updating extensions via the Neurodata Extension Catalog (NDX Catalog), and (3) updating an extension/record.
Boxes shown in gray indicate Git repositories; boxes in orange describe user actions; and boxes in blue indicate actions by administrators of the NDX catalog.
Appendix 3—figure 2
Example ndx-meta.yaml metadata record for the ndx-simulation-output extension.
Appendix 4—figure 1
Overview of select data analysis, visualization, and management tools that support NWB.
Visualization showing select data analysis, visualization, and management tools that support NWB organized by their main application (x-axis) and programming environment (y-axis).
Appendix 7—figure 1
Software Release Process and History.
Overview of the release history of the PyNWB, HDMF, and MatNWB APIs and the NWB and hdmf-common data standard schema.
Tables
Appendix 5—table 1
Compliance of NWB+DANDI with FAIR principles: Findability.
| Findable | ||||
|---|---|---|---|---|
| F1. (Meta)data are assigned a globally unique and persistent identifier | F2. Data are described with rich metadata (defined by R1 below) | F3. Metadata clearly and explicitly include the identifier of the data they describe | F4. (Meta)data are registered or indexed in a searchable resource | |
| Custom | No | No | No |
|
| Zarr | No |
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||
| HDF5 | No | |||
| NIX |
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||
| NWB 1.0 | No |
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| NWB 2 .x |
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| DANDI |
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Appendix 5—table 2
Compliance of NWB+DANDI with FAIR principles: Accessibility.
| Accessible | ||||
|---|---|---|---|---|
| A1. (Meta)data are retrievable by their identifier using a standardised communications protocol | A1.1 The protocol is open, free, and universally implementable | A1.2 The protocol allows for an authentication and authorisation procedure, where necessary | A2. Metadata are accessible, even when the data are no longer available | |
| Custom | No | No |
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| Zarr |
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| HDF5 |
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| NIX |
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| NWB 1.0 |
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| NWB 2 .x |
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| DANDI |
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Appendix 5—table 3
Compliance of NWB+DANDI with FAIR principles: Interoperability.
| Interoperable | |||
|---|---|---|---|
| I1. (Meta)data uses a formal, accessible, shared, and broadly applicable language for knowledge representation. | I2. (Meta)data use vocabularies that follow FAIR principles | I3. (Meta)data include qualified references to other (meta)data | |
| Custom | No | No | No |
| Zarr | No | No | No |
| HDF5 | No | No | No |
| NIX |
|
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|
| NWB 1.0 |
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| NWB 2 .x |
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| DANDI |
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-
*
Support for external resources has been released in HDMF >2.3 and is currently undergoing community review for integration with the NWB core data standard.
Appendix 5—table 4
Compliance of NWB+DANDI with FAIR principles: Reusability.
| Reusable | ||||
|---|---|---|---|---|
| R1. (Meta)data are richly described with a plurality of accurate and relevant attributes | R1.1. (Meta)data are released with a clear and accessible data usage license | R1.2. (Meta)data are associated with detailed provenance | R1.3. (Meta)data meet domain-relevant community standards | |
| Custom | No |
|
No | No |
| Zarr | No | No | No | |
| HDF5 | No | No | No | |
| NIX |
|
No |
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| NWB 1.0 |
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| NWB 2 .x |
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| DANDI |
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