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The Neurodata Without Borders (NWB) initiative promotes data standardization in neuroscience to increase research reproducibility and opportunities. In the first NWB pilot project, neurophysiologists and software developers produced a common data format for recordings and metadata of cellular electrophysiology and optical imaging experiments. The format specification, application programming interfaces, and sample datasets have been released.
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http://dx.doi.org/10.1016/j.neuron.2015.10.025 | DOI Listing |
bioRxiv
July 2025
CatalystNeuro, Casper, WY, USA.
The DANDI Archive is a key resource for sharing open neurophysiology data, hosting over 400 datasets in the Neurodata Without Borders (NWB) format. While these datasets hold tremendous potential for reanalysis and discovery, many researchers face barriers to reuse, including unfamiliarity with access methods and difficulty identifying relevant content. Here we introduce an AI-powered, agentic chat assistant and a notebook generation pipeline.
View Article and Find Full Text PDFSci Data
July 2025
Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Aichi, Japan.
The link between comprehensive behavioral measurements during a behavioral task and brain-wide neuronal activity is an essential strategy to better understand the brain dynamics underlying the emergence of behavior changes. To tackle this, we provide an extensive, multimodal dataset that includes 15 sessions spanning 2 weeks of motor skill learning, in which 25 mice were trained to pull a lever to obtain water rewards. Simultaneous high-speed videography captured body, facial, and eye movements, and environmental parameters were monitored.
View Article and Find Full Text PDFbioRxiv
June 2025
Department of Biomedical Engineering, Johns Hopkins University.
The growing channel count of silicon probes has substantially increased the number of neurons recorded in electrophysiology (ephys) experiments, rendering traditional manual spike sorting impractical. Instead, modern ephys recordings are processed with automated methods that use waveform template matching to isolate putative single neurons. While scalable, automated methods are subject to assumptions that often fail to account for biophysical changes in action potential waveforms, leading to systematic errors.
View Article and Find Full Text PDFPLoS Comput Biol
May 2025
Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
Advancements in calcium indicators and optical techniques have made optical neural recording common in neuroscience. As data volumes grow, streamlining the analysis pipelines for image preprocessing, signal extraction, and subsequent neural activity analyses becomes essential. Challenges in analysis includes 1) ensuring data quality of original and processed data at each step, 2) selecting optimal algorithms and their parameters from numerous options, each with its own pros and cons, by implementing or installing them manually, 3) systematically recording each analysis step for reproducibility, and 4) adopting standard data formats for data sharing and meta-analyses.
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April 2025
Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Key Laboratory of Biomedical Engineering of Education Ministry, Department of Biomedical Engineering, Zhejiang University, Hangzhou, China.
The characteristics of refractory epilepsy change with disease progression. However, relevant studies are scarce due to the difficulty in obtaining long-term multi-site data from patients with epilepsy. This work aimed to provide a long-term brain electrophysiological dataset of 15 pilocarpine-treated rats with temporal lobe epilepsy (TLE).
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