Pynapple, a toolbox for data analysis in neuroscience.

data analysis neuroscience software package systems neuroscience

Journal

eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614

Informations de publication

Date de publication:
16 10 2023
Historique:
medline: 23 10 2023
pubmed: 16 10 2023
entrez: 16 10 2023
Statut: epublish

Résumé

Datasets collected in neuroscientific studies are of ever-growing complexity, often combining high-dimensional time series data from multiple data acquisition modalities. Handling and manipulating these various data streams in an adequate programming environment is crucial to ensure reliable analysis, and to facilitate sharing of reproducible analysis pipelines. Here, we present Pynapple, the PYthon Neural Analysis Package, a lightweight python package designed to process a broad range of time-resolved data in systems neuroscience. The core feature of this package is a small number of versatile objects that support the manipulation of any data streams and task parameters. The package includes a set of methods to read common data formats and allows users to easily write their own. The resulting code is easy to read and write, avoids low-level data processing and other error-prone steps, and is open source. Libraries for higher-level analyses are developed within the Pynapple framework but are contained within a collaborative repository of specialized and continuously updated analysis routines. This provides flexibility while ensuring long-term stability of the core package. In conclusion, Pynapple provides a common framework for data analysis in neuroscience.

Identifiants

pubmed: 37843985
doi: 10.7554/eLife.85786
pii: 85786
pmc: PMC10578930
doi:
pii:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Subventions

Organisme : CIHR
ID : 155957
Pays : Canada
Organisme : CIHR
ID : 180330
Pays : Canada

Informations de copyright

© 2023, Viejo et al.

Déclaration de conflit d'intérêts

GV, DL, SS, DM, SM, GV, HD, LS, FB No competing interests declared, AP Reviewing editor, eLife

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Auteurs

Guillaume Viejo (G)

Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.
Flatiron Institute, Center for Computational Neuroscience, New York, United States.

Daniel Levenstein (D)

Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.
MILA - Quebec IA Institute, Montreal, Canada.

Sofia Skromne Carrasco (S)

Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.

Dhruv Mehrotra (D)

Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.

Sara Mahallati (S)

Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.

Gilberto R Vite (GR)

Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.

Henry Denny (H)

Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.

Lucas Sjulson (L)

Departments of Psychiatry and Neuroscience, Albert Einstein College of Medicine, Bronx, United States.

Francesco P Battaglia (FP)

Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.

Adrien Peyrache (A)

Montreal Neurological Institute and Hospital, McGill University, Montreal, Canada.

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Classifications MeSH