Preclinical and animal research
Animal and preclinical neuroscience accounts for a large share of experimental work, and its open-data infrastructure is partly shared with human neuroscience and partly distinct. Much of that infrastructure is species-agnostic and is more often described in terms of its human applications, so this overview brings the animal-research threads together.
Shared neurophysiology infrastructure
The main open-data tools and standards for animal neurophysiology are shared with human systems neuroscience. NWB (Neurodata Without Borders) is the community standard for neurophysiology data, and its core modalities of extracellular and intracellular electrophysiology, calcium imaging, and optogenetics are predominantly acquired in animal models. DANDI Archive is the open archive that NWB data is submitted to, and most of its holdings are animal-model recordings from NIH BRAIN Initiative projects. Both are species-agnostic by design, which is why they also appear in the Electrophysiology perspective.
Open animal datasets
Two large open mouse datasets are central to animal neurophysiology. The IBL (International Brain Laboratory) releases all of its data and code openly, with its Brain Wide Map of mouse decision-making deposited on DANDI Archive in NWB format. The Allen Institute for Brain Science produces the MindScope Visual Coding and Visual Behavior Neuropixels datasets, large open recordings from the mouse visual system, also packaged in NWB and distributed via DANDI Archive.
Peripheral nervous system
SPARC SDS (SPARC Data Structure) is the data organisation standard for the peripheral and autonomic nervous system, and most data held in it comes from animal studies of how nerves and organs interact. It was built in the pattern of BIDS, covering the electrophysiology, anatomy, connectivity, and imaging data that fall outside the brain-focused scope of BIDS. It is the main data standard dedicated to preclinical neuroscience. Datasets organised this way are shared through the SPARC Portal.
Imaging, genomics and electrophysiology overlap
Animal data also flows through infrastructure that serves other domains. For animal electrophysiology, the BIDS extension proposal BEP032 (BIDS-animal-ephys) defines how to organise recordings from animal models. It is well developed and already usable, with its own validator and folder-structure tools, though it has not yet been formally merged into BIDS. For brain imaging, BIDS is increasingly applied to non-human primate PET and MRI and rodent MRI by adapting the existing standard case by case. In genomics and single-cell work, the Allen Institute for Brain Science and BICAN produce mammalian brain cell atlases deposited in NeMO Archive and CELLxGENE, spanning mouse and other model species.
For the broader electrophysiology landscape, see Electrophysiology. For computational models and morphological reconstructions, many of which derive from animal data, see Computational.