DANDI

Find Dandisets Faster with Advanced Search

Thu, 11 Jun 2026 00:00:00 +0000

Until now, searching the DANDI Archive dandiset list meant typing free text and hoping the words you chose appeared somewhere in a dandiset’s metadata. That works well for finding a dataset you already know by name, but it’s a blunt instrument when you want to ask a more specific question — “Which dandisets have mouse electrophysiology data published since 2024?” or “What has my lab contributed?”

The search box now understands a structured, Gmail/GitHub-style syntax that lets you mix free-text terms with key:value operators. You can filter by creation date, species, file type, contributor, role, funder, affiliation, owner, and more — all from the same input you already use.

Place Cells in Space: Hippocampal Recordings from the Space Shuttle

Fri, 27 Feb 2026 00:00:00 +0000

Navigating Without Gravity

How does the brain know where you are? In mammals, hippocampal “place cells” fire at specific locations, forming an internal map of the environment. These cells rely on a combination of visual landmarks and self-motion cues, including signals from the vestibular system that sense gravity and head orientation, to maintain a stable spatial code.

But what happens when you remove gravity from the equation?

This was the question behind one of the most unusual neuroscience experiments ever conducted. During the Neurolab Space Shuttle mission (STS-90) in April 1998, James Knierim, Bruce McNaughton, and Gina Poe recorded ensembles of hippocampal place cells from three freely moving rats in microgravity, the only recordings of navigation-related neurons from freely behaving animals in space.

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.

Unraveling Anesthesia's Effect on Brain Activity

Sun, 10 Nov 2024 00:00:00 +0000

Data Reuse Highlight:

This blog entry is part of an ongoing series that showcases examples of data reuse and reanalysis using publicly available data on DANDI.

The Original Study: Peering into the Anesthetized Brain

In June 2023, Dr. Leslie Claar and colleagues from the Allen Institute published their groundbreaking findings in the journal eLife in the article, “Cortico-thalamo-cortical interactions modulate electrically evoked EEG responses in mice”. Their approach was comprehensive: they stimulated mouse cortex while simultaneously recording with electroencephelography (EEG) and neuropixels probes, comparing brain activity during wakefulness and under isoflurane anesthesia.

Human ex-vivo microscopy workshop/hackathon

Tue, 08 Mar 2022 00:00:00 +0000

Date/Time: April 21 - 22, 2022. 9am - 6pm ET

Online: Link will be sent to registered participants.

If you are interested in participating please fill in this form to be sent announcements: Register here

Pre-meeting presentations

YouTube Playlist

The Dandisets
- Dandiset 000026 video: Link to dataset
- Dandiset 000108 video: Link to dataset
The Standards
- BIDS-Microscopy video
  - BIDS Microscopy Specification
  - Slides
- OME-NGFF video
  - NGFF Specification
  - Slides
The Tools
- Neuroglancer video: Link to Github repository
- NeuroTrAle video

Agenda for the hackathon

The events will run 9 - 6 ET to accommodate multiple time zones. Participants are welcome to join at any time.

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.

DANDI User Workshop

Wed, 13 Oct 2021 00:00:00 +0000

Click to view a recording of the workshop

Registration is closed

DANDI: A data archive and collaboration space for neurophysiology

Sun, 12 Sep 2021 00:00:00 +0000

DANDI is a US BRAIN Initiative supported data archive for publishing and sharing neurophysiology data including intracellular and extracellular electrophysiology, optophysiology, and behavioral time-series, and images from immunostaining experiments. For example, data from experimental techniques like patch clamps, silicon probes, and calcium imaging can be published on DANDI. So can data from lightsheet microscopy experiments when combined with associated MRI data.

DANDI allows scientists to publish “dandisets,” collections of data from neuroscience experiments that are often associated with specific papers or projects. DANDI is built to scale with the growing data engineering needs of the community and can easily receive and publish TBs of data for free supported by the AWS public dataset program. It also uses best practices in metadata curation using the DANDI schema and allows users to mint DOIs using Datacite for publishing dandisets.

Search Results

Mon, 01 Jan 0001 00:00:00 +0000