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https://github.com/garrettmflynn/webnwb

A JavaScript API for working with neurodata stored in the NWB Format
https://github.com/garrettmflynn/webnwb

Last synced: about 2 months ago
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A JavaScript API for working with neurodata stored in the NWB Format

Host: GitHub
URL: https://github.com/garrettmflynn/webnwb
Owner: garrettmflynn
License: agpl-3.0
Created: 2022-01-12T18:25:36.000Z (about 3 years ago)
Default Branch: main
Last Pushed: 2024-06-06T15:32:40.000Z (8 months ago)
Last Synced: 2024-11-16T00:12:20.084Z (2 months ago)
Language: TypeScript
Homepage: https://brainsatplay.com/webnwb/tutorial
Size: 38.6 MB
Stars: 5
Watchers: 3
Forks: 1
Open Issues: 7
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

        # WebNWB

Neurodata without Borders — directly on the browser.

[![Npm package version](https://badgen.net/npm/v/webnwb)](https://npmjs.com/package/webnwb)

[![Npm package monthly downloads](https://badgen.net/npm/dm/webnwb)](https://npmjs.ccom/package/webnwb)

[![License: AGPL v3](https://img.shields.io/badge/license-AGPL_v3-blue.svg)](https://www.gnu.org/licenses/agpl-3.0)

[![Discord](https://img.shields.io/badge/community-discord-7289da.svg?sanitize=true)](https://discord.gg/CDxskSh9ZB)

`webnwb` is a library for reading and writing Neurodata without Borders (NWB) files on the web.

## Features

- 🔬 Read data from NWB files based on the included specification.

- ⚡ Lazy-load large files (e.g. from the NIH Brain Initiative’s [Distributed Archives for Neurophysiology Data Integration (DANDI)](https://gui.dandiarchive.org/#/)).

- 📦 Create NWB files from scratch.

- ⚒️ Use helper functions like `addAcquisition`, `getAcquisition`, and `createAcquisition` to quickly write data to new and existing NWB files.

> **Note:** While tools like [neurosift] are extraordinarily useful for rapid visualization of NWB files, WebNWB is intended to provide a robust interface for modifying NWB files—a task that requires significantly more preprocessing to accomplish strictly in accordance with the NWB Schema. If you prefer I/O speed, you may wish to look at [hdf5-io], [h5wasm], or other minimal HDF5 readers.

## Documentation

Visit [nwb.brainsatplay.com](https://nwb.brainsatplay.com) for documentation and examples.

## Contributing

The essential features of the WebNWB API are aggregated in the [api.ts](./src/api.ts) file, which configures [hdf5-io] to process the underlying HDF5 file in a way that conforms with the NWB Schema.

Anyone who would like to contribute to the acceptance of `webnwb` as an official NWB API is welcome to message [Garrett Flynn](mailto:garrettmflynn@gmail) to coordinate work on the following areas (or anything else you think will be useful):

1. Validate writing a dataset using [best practices](https://www.nwb.org/best-practices/) and the [schema](https://nwb-schema.readthedocs.io/en/latest/format_description.html#nwbcontainer-nwbdata-nwbdatainterface-base-neurodata-types-for-containers-and-datasets)

2. Allow writing a dataset in place using the File Access API (Chrome)

3. Support Zarr as a backend file format

## Derivative Packages

- [hdf5-io]: Load HDF5 files as JavaScript objects using [h5wasm].

- [apify](./packages/apify/index.ts): A way to generate APIs from simple specification languages (e.g. the NWB Schema)

    - [esconform](https://github.com/garrettmflynn/esconform): A generic library for enforcing schema properties

- [dandi](https://github.com/neuralinterfaces/dandi-js): A basic API for making calls to the DANDI REST API.

- [nwb-inspector](./packages/nwbinspector/README.md): A port of the original NWB Inspector for the browser

## Known Issues

1. `.specloc` is not rewritten as an object reference

2. Sometimes we get a **memory overload error** before the file is completely written. This leads to partial rewrites...

    - Some of these issues might be resolved by moving to the [WorkerFS filesystem](https://github.com/usnistgov/h5wasm/issues/40#issuecomment-1336314071) and uniformly making the API asynchronous.

3. **Links, references, and tables (with references) are not yet supported.**

4. **Cannot save multidimensional arrays** like the data property in a SpatialSeries.

5. **Timestamp arrays can't be written** (e.g. `timestamps` in a TimeSeries) because they are trying to convert to a BigInt by `h5wasm`.

6. Using this library again with Vite will require you to specify `hdf5-io` as excluded from the optimized dependencies: 

```javascript

// vite.config.js

export default defineConfig({

    optimizeDeps: {

        exclude: ['hdf5-io']

    }

})

```

## Acknowledgments

From January to August 2023, the development of **WebNWB** was generously supported by a contract from the [Kavli Foundation](https://kavlifoundation.org/). The basic API was originally prototyped as part of the [2022 NWB-DANDI Remote Developer Hackathon](https://neurodatawithoutborders.github.io/nwb_hackathons/HCK12_2022_Remote/) and refined during the [2022 NWB User Days](https://neurodatawithoutborders.github.io/nwb_hackathons/HCK13_2022_Janelia/) event by [Garrett Flynn](https://github.com/garrettmflynn) from [Brains@Play](https://github.com/brainsatplay).

[hdf5-io]: https://github.com/garrettmflynn/hdf5-io

[h5wasm]: https://github.com/usnistgov/h5wasm

[neurosift]: https://github.com/flatironinstitute/neurosift