Mouse Hippocampal Sharp Wave Ripple Dataset Curated From Public Neuropixels Datasets

Here we present sharp wave ripple (SWR) data derived from neuropixels LFP data from the Allen Brain Institute (ABI) Visual Behavior and Visual Coding datasets1 as well as the International Brain Laboratory (IBL) dataset2,3 in a sharable format which integrates with their APIs. We have extracted, curated using field standards, and shared over 2,054,021 SWR events from 258 mice from these datasets as well as the code used to process them. For collection methods for the original datasets please refer to the following resources and publications. For the ABI Visual Coding and Behavior datasets methods refer to the white papers, and data may be obtained on the DANDI archive4 for Visual Coding5 and Visual Behaviour 6 or through the allensdk 7,8. For the IBL Decision Making Dataset2,3 refer to the white papers for spike sorting9 and behavior10 for experimental methods details the data is hosted on DANDI archive11 and is also available though the ONE-api12,13.

Project was funded by Canadian Institutes of Health Research (CIHR) Foundation Grant FDN-143209 and project grant PJT-180631 to T.H.M. THM was also supported by the Brain Canada Neurophotonics Platform, a Heart and Stroke Foundation of Canada grant in aid, National Science and Engineering Council of Canada (NSERC; GPIN-2022-03723). This work was supported by resources made available through the Dynamic Brain Circuits cluster and the NeuroImaging and NeuroComputation Centre at the UBC Djavad Mowafaghian Centre for Brain Health (RRID SCR_019086) and made use of the DataBinge forum. We thank the Pavlidis lab for generous use of compute and storage resources.

References
1. Siegle, J. H. et al. Survey of spiking in the mouse visual system reveals functional hierarchy. Nature 592, 86–92 (2021).
2. International Brain Laboratory et al. Standardized and reproducible measurement of decision-making in mice. Elife 10, (2021).
3. International Brain Laboratory. Electronic address: [e-mail] & International Brain Laboratory. An International Laboratory for Systems and Computational Neuroscience. Neuron 96, 1213–1218 (2017).
4. DANDI Archive. https://dandiarchive.org/.
5. Baker, Cody DANDI archive. https://dandiarchive.org/dandiset/000728/draft. (2024) Allen Institute - Visual Coding - Optical Physiology (Version draft) [Data set]. DANDI Archive https://dandiarchive.org/dandiset/000728?search=neuropixels&pos=2 (2023).
6. Bennett, C. Allen Institute - Visual Behavior - Neuropixels (2024). (Version 0.240702.1725) [Data set]. DANDI archive. https://doi.org/10.48324/dandi.000713/0.240702.1725 (2024) doi:10.48324/dandi.000713/0.240702.1725.
7. AllenSDK: Code for Reading and Processing Allen Institute for Brain Science Data. (Github).
8. Welcome to the Allen SDK — Allen SDK dev documentation. https://allensdk.readthedocs.io/en/latest/.
9. International Brain Laboratory. Spike sorting pipeline for the International Brain Laboratory. https://doi.org/10.6084/m9.figshare.19705522.v1 (2022).
10. International Brain Laboratory. Video hardware and software for the International Brain Laboratory. https://doi.org/10.6084/m9.figshare.19694452.v1 (2022).
11. Benson, B. et al. International Brain Laboratory; (2024) IBL - Brain Wide Map (Version draft) [Data set]. DANDI archive. https://dandiarchive.org/dandiset/000409/draft (2023).
12. ONE: Open Neurophysiology Environment. (Github).
13. Welcome to ONE’s documentation! — ONE documentation. https://int-brain-lab.github.io/ONE/.

搜集汇总

背景与挑战

背景概述

该数据集是一个从小鼠海马尖波涟漪（SWR）事件中提取和整理的数据集，来源于公开的Neuropixels数据集，包括Allen Brain Institute的Visual Behavior和Visual Coding数据集以及International Brain Laboratory的决策制定数据集。数据集包含超过205万个SWR事件，涉及258只小鼠，并提供了处理代码，旨在以可共享格式整合到相关API中，支持神经科学研究。