Nwb on DANDI

Introducing DANDI Atlas Explorer: Explore the DANDI Archive in 3D

Tue, 24 Feb 2026 00:00:00 +0000

Where in the brain does DANDI have data? As the archive grows, this question becomes increasingly important for researchers planning experiments, searching for collaborators, or surveying available data for meta-analyses. Today, we’re excited to introduce DANDI Atlas Explorer—an interactive 3D brain viewer that lets you explore the DANDI Archive through the lens of the Allen Common Coordinate Framework (CCF) mouse brain atlas.

What is DANDI Atlas Explorer?

DANDI Atlas Explorer is a browser-based tool that renders an interactive 3D mouse brain and highlights which regions have associated neurophysiology datasets on DANDI. Regions with more datasets appear more opaque, giving you an immediate, intuitive sense of data coverage across the brain. Click any region to see the specific dandisets that recorded there, with direct links back to the DANDI Archive.

NWB Compression Recommendations for DANDI Archive

Mon, 03 Nov 2025 00:00:00 +0000

When submitting large datasets to the DANDI Archive, it’s crucial to consider data compression options that can substantially reduce file sizes. Smaller files reduce the storage burden on the DANDI Archive and make datasets more convenient to download for users. Neurodata Without Borders (NWB) now supports two file format backends: HDF5 and Zarr. Both formats have built-in capabilities for chunking and compression that can break large datasets into smaller pieces and apply lossless compression to each chunk. This approach reduces file size without altering the dataset values.

External Links in NWB and DANDI

Thu, 03 Mar 2022 00:00:00 +0000

The need for external files

Neurophysiology experiments often include natural videos (such as behaving animals), which need to be stored with the neurophysiological recordings in order to ensure maximal reusability of the data. These videos are commonly stored with lossy compression (e.g. h264 in an .mp4 file), which allows them to achieve very high compression ratios. It is possible to read these videos frame-by-frame, and store them in HDF5, but since HDF5 is not able to access popular video codecs like h264, the volume of the video in the NWB file is much larger (even when using the available compression algorithms like GZIP). NWB has an option to avoid storing these altogether by linking to these external video files using a relative path to that file on disk. This relative path is stored in the ImageSeries neurodata_type storing it as an attribute of a string dtype. We also need to publish these video linked NWB files in an archive (e.g. in DANDI). For DANDI, which renames and reorganizes the the NWB files, this requires not only uploading the video file on the archive but also changing the path attribute of the ImageSeries to reflect the new file names.