Literature DB >> 32132545

A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task.

N Chandravadia1, D Liang2, A G P Schjetnan3, A Carlson1, M Faraut1, J M Chung4, C M Reed4, B Dichter5,6, U Maoz2,7, S K Kalia3,8, T A Valiante3,8, A N Mamelak1, U Rutishauser9,10,11,12,13.   

Abstract

A challenge for data sharing in systems neuroscience is the multitude of different data formats used. Neurodata Without Borders: Neurophysiology 2.0 (NWB:N) has emerged as a standardized data format for the storage of cellular-level data together with meta-data, stimulus information, and behavior. A key next step to facilitate NWB:N adoption is to provide easy to use processing pipelines to import/export data from/to NWB:N. Here, we present a NWB-formatted dataset of 1863 single neurons recorded from the medial temporal lobes of 59 human subjects undergoing intracranial monitoring while they performed a recognition memory task. We provide code to analyze and export/import stimuli, behavior, and electrophysiological recordings to/from NWB in both MATLAB and Python. The data files are NWB:N compliant, which affords interoperability between programming languages and operating systems. This combined data and code release is a case study for how to utilize NWB:N for human single-neuron recordings and enables easy re-use of this hard-to-obtain data for both teaching and research on the mechanisms of human memory.

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Year:  2020        PMID: 32132545      PMCID: PMC7055261          DOI: 10.1038/s41597-020-0415-9

Source DB:  PubMed          Journal:  Sci Data        ISSN: 2052-4463            Impact factor:   6.444


  17 in total

1.  Neurodata Without Borders: Creating a Common Data Format for Neurophysiology.

Authors:  Jeffery L Teeters; Keith Godfrey; Rob Young; Chinh Dang; Claudia Friedsam; Barry Wark; Hiroki Asari; Simon Peron; Nuo Li; Adrien Peyrache; Gennady Denisov; Joshua H Siegle; Shawn R Olsen; Christopher Martin; Miyoung Chun; Shreejoy Tripathy; Timothy J Blanche; Kenneth Harris; György Buzsáki; Christof Koch; Markus Meister; Karel Svoboda; Friedrich T Sommer
Journal:  Neuron       Date:  2015-11-18       Impact factor: 17.173

2.  European data format 'plus' (EDF+), an EDF alike standard format for the exchange of physiological data.

Authors:  Bob Kemp; Jesus Olivan
Journal:  Clin Neurophysiol       Date:  2003-09       Impact factor: 3.708

3.  In vivo delineation of subdivisions of the human amygdaloid complex in a high-resolution group template.

Authors:  J Michael Tyszka; Wolfgang M Pauli
Journal:  Hum Brain Mapp       Date:  2016-11       Impact factor: 5.038

4.  Single neuron activity in human hippocampus and amygdala during recognition of faces and objects.

Authors:  I Fried; K A MacDonald; C L Wilson
Journal:  Neuron       Date:  1997-05       Impact factor: 17.173

Review 5.  Testing Models of Human Declarative Memory at the Single-Neuron Level.

Authors:  Ueli Rutishauser
Journal:  Trends Cogn Sci       Date:  2019-04-25       Impact factor: 20.229

6.  Simultaneous Eye Tracking and Single-Neuron Recordings in Human Epilepsy Patients.

Authors:  Shuo Wang; Nand Chandravadia; Adam N Mamelak; Ueli Rutishauser
Journal:  J Vis Exp       Date:  2019-06-17       Impact factor: 1.355

7.  Online detection and sorting of extracellularly recorded action potentials in human medial temporal lobe recordings, in vivo.

Authors:  Ueli Rutishauser; Erin M Schuman; Adam N Mamelak
Journal:  J Neurosci Methods       Date:  2006-02-20       Impact factor: 2.390

8.  Single-trial learning of novel stimuli by individual neurons of the human hippocampus-amygdala complex.

Authors:  Ueli Rutishauser; Adam N Mamelak; Erin M Schuman
Journal:  Neuron       Date:  2006-03-16       Impact factor: 17.173

9.  Dataset of human medial temporal lobe single neuron activity during declarative memory encoding and recognition.

Authors:  Mailys C M Faraut; April A Carlson; Shannon Sullivan; Oana Tudusciuc; Ian Ross; Chrystal M Reed; Jeffrey M Chung; Adam N Mamelak; Ueli Rutishauser
Journal:  Sci Data       Date:  2018-02-13       Impact factor: 6.444

10.  Spike sorting for large, dense electrode arrays.

Authors:  Cyrille Rossant; Shabnam N Kadir; Dan F M Goodman; John Schulman; Maximilian L D Hunter; Aman B Saleem; Andres Grosmark; Mariano Belluscio; George H Denfield; Alexander S Ecker; Andreas S Tolias; Samuel Solomon; Gyorgy Buzsaki; Matteo Carandini; Kenneth D Harris
Journal:  Nat Neurosci       Date:  2016-03-14       Impact factor: 24.884

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  5 in total

1.  A NWB-based dataset and processing pipeline of human single-neuron activity during a declarative memory task.

Authors:  N Chandravadia; D Liang; A G P Schjetnan; A Carlson; M Faraut; J M Chung; C M Reed; B Dichter; U Maoz; S K Kalia; T A Valiante; A N Mamelak; U Rutishauser
Journal:  Sci Data       Date:  2020-03-04       Impact factor: 6.444

2.  The Neurodata Without Borders ecosystem for neurophysiological data science.

Authors:  Oliver Rübel; Andrew Tritt; Ryan Ly; Benjamin K Dichter; Satrajit Ghosh; Lawrence Niu; Pamela Baker; Ivan Soltesz; Lydia Ng; Karel Svoboda; Loren Frank; Kristofer E Bouchard
Journal:  Elife       Date:  2022-10-04       Impact factor: 8.713

3.  Dataset of cortical activity recorded with high spatial resolution from anesthetized rats.

Authors:  Csaba Horváth; Lili Fanni Tóth; István Ulbert; Richárd Fiáth
Journal:  Sci Data       Date:  2021-07-15       Impact factor: 6.444

4.  Dataset of human intracranial recordings during famous landmark identification.

Authors:  Oscar Woolnough; Cihan M Kadipasaoglu; Christopher R Conner; Kiefer J Forseth; Patrick S Rollo; Matthew J Rollo; Vatche G Baboyan; Nitin Tandon
Journal:  Sci Data       Date:  2022-01-31       Impact factor: 6.444

5.  Single-neuron correlate of epilepsy-related cognitive deficits in visual recognition memory in right mesial temporal lobe.

Authors:  Seung J Lee; Danielle E Beam; Andrea G P Schjetnan; Lynn K Paul; Nand Chandravadia; Chrystal M Reed; Jeffrey M Chung; Ian B Ross; Taufik A Valiante; Adam N Mamelak; Ueli Rutishauser
Journal:  Epilepsia       Date:  2021-07-21       Impact factor: 5.864

  5 in total

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