Journal ArticleDOI
Survey of spiking in the mouse visual system reveals functional hierarchy
Joshua H. Siegle,Xiaoxuan Jia,Séverine Durand,Sam Gale,Corbett Bennett,Nile Graddis,Greggory Heller,Tamina K. Ramirez,Hannah Choi,Hannah Choi,Jennifer Luviano,Peter A. Groblewski,Ruweida Ahmed,Anton Arkhipov,Amy Bernard,Yazan N. Billeh,Dillan Brown,Michael A. Buice,Nicolas Cain,Shiella Caldejon,Linzy Casal,Andrew Cho,Maggie Chvilicek,Timothy C. Cox,Kael Dai,Daniel J. Denman,Daniel J. Denman,Saskia E. J. de Vries,Roald Dietzman,Luke Esposito,Colin Farrell,David Feng,John Galbraith,Marina Garrett,Emily Gelfand,Nicole Hancock,Julie A. Harris,Robert Howard,Brian Hu,Ross Hytnen,Ramakrishnan Iyer,Erika Jessett,Katelyn Johnson,India Kato,Justin T. Kiggins,Sophie Lambert,Jérôme Lecoq,Peter Ledochowitsch,Jung Hoon Lee,Arielle Leon,Yang Li,Elizabeth Liang,Fuhui Long,Kyla Mace,Jose Melchior,Daniel Millman,Tyler Mollenkopf,Chelsea Nayan,Lydia Ng,Kiet Ngo,Thuyahn Nguyen,Philip R. Nicovich,Kat North,Gabriel Koch Ocker,Douglas R. Ollerenshaw,Michael Oliver,Marius Pachitariu,Jed Perkins,Melissa Reding,David Reid,Miranda Robertson,Kara Ronellenfitch,Sam Seid,Cliff Slaughterbeck,Michelle Stoecklin,David Sullivan,Ben Sutton,Jackie Swapp,Carol L. Thompson,Kristen Turner,Wayne Wakeman,Jennifer D. Whitesell,Derric Williams,Ali Williford,R.D. Young,Hongkui Zeng,Sarah A. Naylor,John W. Phillips,R. Clay Reid,Stefan Mihalas,Shawn R. Olsen,Christof Koch +91 more
TLDR
In this paper, a large-scale dataset of tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli is presented.Abstract:
The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically1. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset-part of the Allen Brain Observatory2-that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli. Using cross-correlation analysis, we reveal that the organization of inter-area functional connectivity during visual stimulation mirrors the anatomical hierarchy from the Allen Mouse Brain Connectivity Atlas3. We find that four classical hierarchical measures-response latency, receptive-field size, phase-locking to drifting gratings and response decay timescale-are all correlated with the hierarchy. Moreover, recordings obtained during a visual task reveal that the correlation between neural activity and behavioural choice also increases along the hierarchy. Our study provides a foundation for understanding coding and signal propagation across hierarchically organized cortical and thalamic visual areas.read more
Citations
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Journal ArticleDOI
Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings
Nicholas A. Steinmetz,Nicholas A. Steinmetz,Cagatay Aydin,Anna Lebedeva,Michael S. Okun,Michael S. Okun,Marius Pachitariu,Marius Bauza,Maxime Beau,Jai Bhagat,Claudia Böhm,Martijn Broux,Susu Chen,Jennifer Colonell,Richard J. Gardner,Bill Karsh,Fabian Kloosterman,Dimitar Kostadinov,Carolina Mora-Lopez,John O'Callaghan,Junchol Park,Jan Putzeys,Britton Sauerbrei,Rik van Daal,Abraham Z. Vollan,Shiwei Wang,Marleen Welkenhuysen,Zhiwen Ye,Joshua T. Dudman,B. Dutta,Adam W. Hantman,Kenneth D. Harris,Albert K. Lee,Edvard I. Moser,John O'Keefe,Alfonso Renart,Karel Svoboda,Michael Häusser,Sebastian Haesler,Sebastian Haesler,Matteo Carandini,Timothy D. Harris +41 more
TL;DR: A suite of electrophysiological tools comprising a miniaturized high-density probe, recoverable chronic implant fixtures, and algorithms for automatic post hoc motion correction are demonstrated, enabling an order-of-magnitude increase in the number of sites that can be recorded in small animals, such as mice, and the ability to record from them stably over long time scales.
Journal ArticleDOI
A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation.
Zizhen Yao,Cindy T. J. van Velthoven,Thuc Nghi Nguyen,Jeff Goldy,Adriana E. Sedeno-Cortes,Fahimeh Baftizadeh,Darren Bertagnolli,Tamara Casper,Megan Chiang,Kirsten Crichton,Songlin Ding,Olivia Fong,Emma Garren,Alexandra Glandon,Nathan W. Gouwens,James Gray,Lucas T. Graybuck,Michael Hawrylycz,Daniel Hirschstein,Matthew Kroll,Kanan Lathia,Changkyu Lee,Boaz P. Levi,Delissa McMillen,Stephanie Mok,Thanh Pham,Qingzhong Ren,Christine Rimorin,Nadiya V. Shapovalova,Josef Sulc,Susan M. Sunkin,Michael Tieu,Amy Torkelson,Herman Tung,Katelyn Ward,Nick Dee,Kimberly A. Smith,Bosiljka Tasic,Hongkui Zeng +38 more
TL;DR: The isocortex and hippocampal formation (HPF) in the mammalian brain play critical roles in perception, cognition, emotion, and learning as discussed by the authors, and a transcriptomic cell type taxonomy revealing a comprehensive repertoire of glutamatergic and GABAergic neuron types.
Posted Content
Large-scale neural recordings call for new insights to link brain and behavior
TL;DR: In this paper, the authors describe emerging tools and technologies being used to probe large-scale brain activity and new approaches to characterize behavior in the context of such measurements, and highlight insights obtained from largescale neural recordings in diverse model systems.
Journal ArticleDOI
Large-scale neural recordings call for new insights to link brain and behavior
TL;DR: In this article , the authors describe emerging tools and technologies being used to probe large-scale brain activity and new approaches to characterize behavior in the context of such measurements, and elaborate on existing modeling frameworks to interpret these data and argue that the interpretation of brain-wide neural recordings calls for new theoretical approaches that may depend on the desired level of understanding.
Journal ArticleDOI
Representational drift in the mouse visual cortex.
TL;DR: In this article, the authors analyzed large-scale optical and electrophysiological recordings from six visual cortical areas in behaving mice that were repeatedly presented with the same natural movies and found representational drift over timescales spanning minutes to days across multiple visual areas, cortical layers, and cell types.
References
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Scikit-learn: Machine Learning in Python
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TL;DR: Scikit-learn is a Python module integrating a wide range of state-of-the-art machine learning algorithms for medium-scale supervised and unsupervised problems, focusing on bringing machine learning to non-specialists using a general-purpose high-level language.
Journal ArticleDOI
Matplotlib: A 2D Graphics Environment
TL;DR: Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.
Journal ArticleDOI
Receptive fields, binocular interaction and functional architecture in the cat's visual cortex
David H. Hubel,Torsten N. Wiesel +1 more
TL;DR: This method is used to examine receptive fields of a more complex type and to make additional observations on binocular interaction and this approach is necessary in order to understand the behaviour of individual cells, but it fails to deal with the problem of the relationship of one cell to its neighbours.
Journal ArticleDOI
The NumPy Array: A Structure for Efficient Numerical Computation
TL;DR: In this article, the authors show how to improve the performance of NumPy arrays through vectorizing calculations, avoiding copying data in memory, and minimizing operation counts, which is a technique similar to the one described in this paper.
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