Spyglass: a framework for reproducible and shareable neuroscience research DOI Creative Commons
Kyu Hyun Lee, Eric L. Denovellis, Ryan Ly

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Янв. 26, 2024

Abstract Scientific progress depends on reliable and reproducible results. Progress can also be accelerated when data are shared re-analyzed to address new questions. Current approaches storing analyzing neural typically involve bespoke formats software that make replication, as well the subsequent reuse of data, difficult if not impossible. To these challenges, we created Spyglass , an open-source framework enables analyses sharing both intermediate final results within across labs. uses Neurodata Without Borders (NWB) standard includes pipelines for several core in neuroscience, including spectral filtering, spike sorting, pose tracking, decoding. It easily extended apply existing newly developed datasets from multiple sources. We demonstrate features context a cross-laboratory replication by applying advanced state space decoding algorithms publicly available data. New users try out Jupyter Hub hosted HHMI 2i2c: https://spyglass.hhmi.2i2c.cloud/ .

Язык: Английский

Prefrontal cortical ripples mediate top-down suppression of hippocampal reactivation during sleep memory consolidation DOI
Justin D. Shin, Shantanu P. Jadhav

Current Biology, Год журнала: 2024, Номер 34(13), С. 2801 - 2811.e9

Опубликована: Июнь 3, 2024

Язык: Английский

Процитировано

6
Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis DOI Creative Commons
Taiga Abe,

Ian Kinsella,

Shreya Saxena

и другие.

Neuron, Год журнала: 2022, Номер 110(17), С. 2771 - 2789.e7

Опубликована: Июль 22, 2022

Язык: Английский

Процитировано

27
Cortico-thalamo-cortical interactions modulate electrically evoked EEG responses in mice DOI Creative Commons
Leslie D. Claar, Irene Rembado,

Jacqulyn R. Kuyat

и другие.

eLife, Год журнала: 2023, Номер 12

Опубликована: Июнь 26, 2023

Perturbational complexity analysis predicts the presence of consciousness in volunteers and patients by stimulating brain with brief pulses, recording EEG responses, computing their spatiotemporal complexity. We examined underlying neural circuits mice directly cortex while Neuropixels probes during wakefulness isoflurane anesthesia. When are awake, stimulation deep cortical layers reliably evokes locally a pulse excitation, followed biphasic sequence 120 ms profound off period rebound excitation. A similar pattern, partially attributed to burst spiking, is seen thalamic nuclei associated pronounced late component evoked EEG. infer that cortico-thalamo-cortical interactions drive long-lasting signals elicited awake state. The EEG, reduced running absent

Язык: Английский

Процитировано

14
Extrinsic control of the early postnatal CA1 hippocampal circuits DOI Creative Commons
Erwan Leprince,

Robin F. Dard,

Salomé Mortet

и другие.

Neuron, Год журнала: 2023, Номер 111(6), С. 888 - 902.e8

Опубликована: Янв. 5, 2023

Язык: Английский

Процитировано

13
Cortico-thalamo-cortical interactions modulate electrically evoked EEG responses in mice DOI Creative Commons
Leslie D. Claar, Irene Rembado,

Jacqulyn R. Kuyat

и другие.

eLife, Год журнала: 2023, Номер 12

Опубликована: Фев. 9, 2023

Perturbational complexity analysis predicts the presence of consciousness in volunteers and patients by stimulating brain with brief pulses, recording EEG responses, computing their spatiotemporal complexity. We examined underlying neural circuits mice directly cortex while Neuropixels probes during wakefulness isoflurane anesthesia. When are awake, stimulation deep cortical layers reliably evokes locally a pulse excitation, followed biphasic sequence 120 ms profound off period rebound excitation. A similar pattern, partially attributed to burst spiking, is seen thalamic nuclei associated pronounced late component evoked EEG. infer that cortico-thalamo-cortical interactions drive long-lasting signals elicited awake state. The EEG, reduced running absent

Язык: Английский

Процитировано

12
The past, present and future of neuroscience data sharing: a perspective on the state of practices and infrastructure for FAIR DOI Creative Commons
Maryann E. Martone

Frontiers in Neuroinformatics, Год журнала: 2024, Номер 17

Опубликована: Янв. 5, 2024

Neuroscience has made significant strides over the past decade in moving from a largely closed science characterized by anemic data sharing, to open where amount of publicly available neuroscience increased dramatically. While this increase is driven part large prospective sharing studies, we are starting see long tail data, no doubt journal requirements and funder mandates. Concomitant with shift increasing support FAIR principles practices infrastructure. particularly critical for its multiplicity types, scales model systems infrastructure that serves them. As envisioned early days neuroinformatics, currently served globally distributed ecosystem neuroscience-centric repositories, specialized around types. To make findable, accessible, interoperable, reusable requires coordination across different stakeholders, including researchers who produce repositories it available, aggregators indexers field search engines community organizations help coordinate efforts develop standards FAIR. The International Neuroinformatics Coordinating Facility led move toward FAIR, fielding several resources achieve In perspective, I provide an overview components required thoughts on past, present future neuroscience, laboratory engine.

Язык: Английский

Процитировано

4
A modular and adaptable analysis pipeline to compare slow cerebral rhythms across heterogeneous datasets DOI Creative Commons
Robin Gutzen, G. De Bonis, Chiara De Luca

и другие.

Cell Reports Methods, Год журнала: 2024, Номер 4(1), С. 100681 - 100681

Опубликована: Янв. 1, 2024

Язык: Английский

Процитировано

4
Dataset of human-single neuron activity during a Sternberg working memory task DOI Creative Commons
Michael Kyzar, Jan Kamiński, Aneta Brzezicka

и другие.

Scientific Data, Год журнала: 2024, Номер 11(1)

Опубликована: Янв. 18, 2024

Abstract We present a dataset of 1809 single neurons recorded from the human medial temporal lobe (amygdala and hippocampus) frontal (anterior cingulate cortex, pre-supplementary motor area, ventral prefrontal cortex) across 41 sessions 21 patients that underwent seizure monitoring with depth electrodes. Subjects performed screening task (907 neurons) to identify images for which highly selective cells were present. then working memory (902 neurons), in they sequentially presented 1–3 and, following maintenance period, asked if probe was identical one maintained images. This Neurodata Without Borders formatted includes spike times, extracellular waveforms, stimuli presented, behavior, electrode locations, subject demographics. As validation, we replicate previous findings on selectivity concept their persistent activity during maintenance. large rare single-neuron recordings behavior enables investigation neural mechanisms humans.

Язык: Английский

Процитировано

4
Unifying community whole-brain imaging datasets enables robust neuron identification and reveals determinants of neuron position in C. elegans DOI Creative Commons
Daniel Sprague, Kevin Rusch, Raymond L. Dunn

и другие.

Cell Reports Methods, Год журнала: 2025, Номер unknown, С. 100964 - 100964

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

0
Modeling Organoid Population Electrophysiology Dynamics DOI Creative Commons
Matthew J. Roos, Daniel Luna, Dowlette‐Mary Alam El Din

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Март 2, 2025

ABSTRACT Improving models to investigate neurodegenerative disease, neurodevelopmental neuro-toxicology and neuropharmacology is critical improve our basic understanding of the human nervous system, as well accelerate discovery interventions drugs. Improved central system could enable discoveries related functional changes induced by sensory stimulation or toxic exposures. Neural organoids, complex three-dimensional cell cultures derived from adult stem cells, have been grown with connectivity neuroanatomy. Moreover, these interfaced bi-directional electrical recording, chemical stimulation. This effort sought develop new computational techniques which be applied comparative studies using neural organoids. In particular, we adapted CEBRA, a state art model in vivo modeling literature, generate 2D 3D embeddings (projections into structured low-dimensional spaces) high dimensional organoid electrophysiology data. can done an unsupervised semi-supervised manner. Results indicate quickly reliably generated serve low-dimensional, interpretable for characterizing activity over time, clustering results around known bursting phenomena. demonstrate that mixtures von Mises-Fisher distributions used parametric embedding spaces statistics hypothesis testing. technique may types creating representation quantitative comparison validation against animal Looking ahead, this work allow formulation class experiments investigating impact toxins, genetic manipulations, pharmacological on neurons.

Язык: Английский

Процитировано

0