Publications

2024

van Beest, Bimbard, Fabre, Dodgson, Takacs, Coen, Lebedeva, Harris, and Carandini, Tracking neurons across days with high-density probes, Nature Methods

Carandini, Sensory choices as logistic classification, Neuron

Bimbard, ..., Carandini, and Coen, An adaptable, reusable, and light implant for chronic Neuropixels probes, eLife

International Brain Laboratory et al, Reproducibility of in vivo electrophysiological measurements in mice, eLife

Ye, Shelton, … , Steinmetz, Ultra-high density electrodes improve detection, yield, and cell type identification in neuronal recordings, bioRxiv

2023

Wool, Lak, Carandini, and Harris, Mouse frontal cortex nonlinearly encodes sensory stimuli, choices, and outcomes, Wellcome Open Research

International Brain Laboratory et al, A brain-wide map of neural activity during complex behaviour, bioRxiv

Findling, Hubert, International Brain Laboratory et al, Brain-wide representations of prior information in mouse decision-making, bioRxiv

Coen, Sit, Wells, Carandini, and Harris, Mouse frontal cortex mediates additive multisensory decisions, Neuron

Bimbard, Sit, Lebedeva, Bai Reddy, Harris, and Carandini, Behavioral origin of sound-evoked activity in visual cortex, Nature Neuroscience

2022

Carandini, Some tips for writing science, eNeuro

Peters, Marica, Fabre, Harris, and Carandini, Visuomotor learning promotes visually evoked activity in the medial prefrontal cortex, Cell Reports

Bugeon, Duffield, Dipoppa, Prankerd …, Isogai, Carandini, and Harris, A transcriptomic axis predicts state modulation of cortical interneurons, Nature

Lee, Krumin, Harris, and Carandini, Task specificity in mouse parietal cortex, Neuron

Nunez-Elizalde, Krumin, Bai Reddy, Montaldo, Urban, Harris, and Carandini, Neural correlates of blood flow measured by ultrasound, Neuron

2021

Zatka-Haas, Steinmetz, Carandini, and Harris, Sensory coding and the causal impact of mouse cortex in a visual decision, eLife

Moss, Zatka-Haas, Harris, Carandini, and Lak, Dopamine axons to dorsal striatum encode contralateral stimuli and actions, J Neurosci

Failor, Carandini, and Harris, Learning orthogonalizes visual cortical population codes, bioRxiv

International Brain Laboratory et al, Standardized and reproducible measurement of decision-making in mice, eLife

Steinmetz, Aydin, Lebedeva, Okun, Pachitariu…. Carandini, and TD Harris, Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings, Science

Diamanti, Bai Reddy, Schröder, Muzzu, Harris, Saleem, and Carandini, Spatial modulation of visual signals arises in cortex with active navigation, eLife

Peters, Fabre, Steinmetz, Harris, and Carandini, Striatal activity topographically reflects cortical activity patterns, Nature

2020

Rossi, Harris, and Carandini, Spatial connectivity matches direction selectivity in visual cortex, Nature

Jacobs, Steinmetz, Carandini, and Harris, Cortical state fluctuations during sensory decision making, Current Biology

Fournier, Saleem, Diamanti, Wells, Harris, and Carandini, Mouse visual cortex is modulated by distance traveled and by theta oscillations, Current Biology

Schröder, Steinmetz, Krumin, Pachitariu, Rizzi, Lagnado, Harris, and Carandini, Arousal modulates retinal output, Neuron

Lak, …, Carandini, Tonegawa, Uchida, and Kepecs, Confidence-guided updating of choice bias during perceptual decisions, eLife

Bhagat, Wells, Peters, Harris, Carandini, and Burgess, Rigbox: An Open-Source Toolbox for Probing Neurons and Behavior, eNeuro

Lin, Okun, Carandini, and Harris, Equations governing dynamics of excitation and inhibition in the mouse corticothalamic network, bioRxiv

2019

Lak, Okun, Moss, Gurnani, Wells, Bai Reddy, Kepecs, Harris, and Carandini, Dopaminergic and prefrontal basis of learning from sensory confidence and reward value, Neuron

Steinmetz, Zatka-Haas, Carandini, and Harris, Distributed coding of choice, action, and engagement across the mouse brain, Nature

Stringer, Pachitariu, Steinmetz, Carandini, and Harris, High-dimensional geometry of population responses in visual cortex, Nature

Carandini, Charting the structure of neuroscience, [web app], Neuron

Shimaoka, Steinmetz, Harris, and Carandini, The impact of bilateral ongoing activity on evoked responses in mouse cortex, eLife

Stringer, Pachitariu, Steinmetz, Bai Reddy, Carandini, and Harris, Spontaneous behaviors drive multidimensional, brain-wide population activity, Science

2018

Krumin, Lee, Harris, and Carandini, Decision and navigation in mouse parietal cortex [video1, video2], eLife

Saleem, Diamanti, Fournier, Harris, and Carandini, Coherent representations of subjective spatial position in primary visual cortex and hippocampus, Nature

Dipoppa, Ranson, Krumin, Pachitariu, Carandini, and Harris, Vision and locomotion shape the interactions between neuron types in mouse visual cortex, Neuron

Shimaoka, Harris, and Carandini Effects of arousal on mouse sensory cortex depend on modality, Cell Reports

Steinmetz, Koch, Harris, and Carandini, Challenges and opportunities for large-scale electrophysiology with Neuropixels probes, Curr Op Neurobiol

2017

The International Brain Laboratory, An international laboratory for systems and computational neuroscience, Neuron

Jun, Steinmetz, Siegle, Denman, Bauza, ..., Carandini, Harris, Koch, O'Keefe, and Harris, Fully integrated silicon probes for high-density recording of neural activity, Nature

Steinmetz, ..., Zeng, Hausser, Carandini, and Harris, Aberrant Cortical Activity In Multiple GCaMP6-Expressing Transgenic Mouse Lines, eNeuro

Burgess, Lak, Steinmetz, Zatka-Haas, Bai Reddy, Jacobs, Linden, Paton, Ranson, Schröder, Soares, Wells, Wool, Harris, and Carandini, High-yield methods for accurate two-alternative visual psychophysics in head-fixed mice, Cell Reports

Rossi, Wykes, Kullmann, and Carandini, Focal cortical seizures start as standing waves and propagate respecting homotopic connectivity, Nature Communications

Saleem, Lien, Krumin, Haider, Roman Roson, Ayaz, Reinhold, Busse, Carandini, and Harris, Subcortical origin and modulation of the narrowband gamma oscillation in mouse visual cortex, Neuron. [failed cover].

Pachitariu, Stringer, Schröder, Dipoppa, Rossi, Carandini, and Harris, Suite2p: beyond 10,000 neurons with standard two-photon microscopy, bioRxiv

2016

Pachitariu, Steinmetz, Kadir, Carandini, and Harris, Kilosort: realtime spike-sorting for extracellular electrophysiology with hundreds of channels, bioRxiv

Abrahamyan, Silva, Dakin, Carandini, and Gardner, Adaptable history biases in human perceptual decisions, PNAS

Haider, Schulz, Häusser, and Carandini, Millisecond coupling of local field potentials to synaptic currents in the awake visual cortex, Neuron

Pisauro, Benucci, and Carandini, Local and global contributions to hemodynamic activity in mouse cortex, J Neurophysiol

Rossant, Kadir, Goodman, …,Carandini, and Harris, Spike sorting for large, dense electrode arrays, Nature Neuroscience

Sato, Haider, Häusser, and Carandini, An excitatory basis for divisive normalization in visual cortex, Nature Neuroscience

Okun, Lak, Carandini, and Harris, Long term recordings with immobile silicon probes in the mouse cortex, PLoS ONE

Carandini, Light adaptation explains different linearity of ON and OFF responses, bioRxiv

Ganmor, Krumin, Rossi, Carandini, and Simoncelli, Direct estimation of firing rates from calcium imaging data, arXiv

2015

Lin, Okun, Carandini, and Harris, The nature of shared cortical variability, Neuron

Schulz, Sahani, and Carandini, Five key factors determining pairwise correlations in visual cortex, J Neurophysiol

Okun, Steinmetz, …, Mrsic-Flogel, Carandini, and Harris, Diverse coupling of neurons to populations in sensory cortex, Nature

Madisen, Garner, Shimaoka,…, Reid, Carandini, and Zeng, Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance. Neuron

Carandini, Shimaoka, Rossi, Sato, Benucci, and Knöpfel, Imaging the awake visual cortex with a genetically-encoded voltage indicator, J Neurosci

Schölvinck, Saleem, Benucci, Harris, and Carandini, Cortical state determines global variability and correlations in visual cortex, J Neurosci

2014

Schröder and Carandini, A cortical rein on the tectum's gain, Neuron

Dhruv and Carandini, Cascaded effects of spatial adaptation in the early visual system, Neuron

Sato, Häusser, and Carandini, Distal connectivity causes summation and division across mouse visual cortex, Nature Neuroscience

2013

Pisauro, Dhruv, Carandini, and Benucci, Fast hemodynamic responses in the visual cortex of the awake mouse, J Neurosci.

Saleem, Ayaz, Jeffery, Harris, and Carandini, Integration of visual motion and locomotion in mouse visual cortex, Nature Neuroscience.

Carandini and Churchland, Probing perceptual decisions in rodents, Nature Neuroscience.

Ayaz, Saleem, Schölvinck, and Carandini, Locomotion controls spatial integration in mouse visual cortex, Current Biology.

Benucci, Saleem, and Carandini, Adaptation maintains population homeostasis in primary visual cortex, Nature Neuroscience.

Haider, Häusser, and Carandini, Inhibition dominates sensory responses in the awake cortex, Nature.

2012

Okun, Yger, Marguet, Gerard-Mercier, Benucci, Katzner, Busse, Carandini, and Harris, Population rate dynamics and multineuron firing patterns in sensory cortex [Code], J Neurosci.

Sato, Nauhaus and Carandini, Traveling waves in visual cortex, Neuron.

Pearson, Barber, ..., Benucci, ..., Carandini, Yau, Sowden, and Ali, Restoration of vision after transplantation of photoreceptors, Nature.

Carandini, From circuits to behavior: a bridge too far?, Nature Neuroscience.

Nauhaus, Busse, Ringach, and Carandini, Robustness of traveling waves in ongoing activity of visual cortex, J Neurosci.

Carandini, Area V1, Scholarpedia.

Atallah, Bruns, Carandini, and Scanziani, Parvalbumin-expressing interneurons linearly transform cortical responses to visual stimuli, Neuron.

Carandini and Heeger, Normalization as a canonical neural computation, Nature Reviews Neuroscience.

2011

Busse, Ayaz, Dhruv, Katzner, Saleem, Schölvinck, Zaharia, and Carandini, The detection of visual contrast in the behaving mouse [video], J Neurosci.

Katzner, Busse, and Carandini, GABAa inhibition controls response gain in visual cortex, J Neurosci.

2010

Schulz and Carandini, An uncorrelated state for the cortex?, F1000 Biology Reports.

2009

Busse, Wade, and Carandini, Representation of concurrent stimuli by population activity in visual cortex [Supplementary], Neuron.

Benucci, Ringach, and Carandini, Coding of stimulus sequences by population responses in visual cortex [Supplem video], Nature Neuroscience.

Katzner, Nauhaus, Benucci, Bonin, Ringach, and Carandini, Local origin of field potentials in visual cortex, Neuron.

Nauhaus, Busse, Carandini, and Ringach, Stimulus contrast modulates functional connectivity in visual cortex, Nature Neuroscience.

2008

Mante, Bonin, and Carandini, Functional mechanisms shaping lateral geniculate responses to artificial and natural stimuli [failed cover][CatCam video][Tarzan video], Neuron.

Nauhaus, Benucci, Carandini, and Ringach, Neuronal selectivity and local map structure in visual cortex, Neuron. [failed cover].

2007

Carandini, Horton, and Sincich, Thalamic filtering of retinal spike trains by postsynaptic summation, J of Vision.

Benucci, Frazor, and Carandini, Standing waves and traveling waves distinguish two circuits in visual cortex, Neuron.

Frazor, Benucci, and Carandini, Independent Encoding of Position and Orientation by Population Responses in Primary Visual Cortex, in Advances in Brain, Vision, and Artificial Intelligence, pp. 30-41, Springer.

Durand, Freeman, and Carandini, Temporal properties of surround suppression in cat primary visual cortex, Visual Neuroscience.

Majaj, Carandini, and Movshon, Motion integration by neurons in macaque MT is local, not global, J Neurosci.

Carandini, Melting the iceberg: contrast invariance in visual cortex, Neuron.

2006

Bonin, Mante, and Carandini, The statistical computation underlying contrast gain control, J Neurosci.

Carandini, What simple cells and complex cells compute, J Physiol.

Carandini, Measuring the brain's assumptions, Nature Neuroscience.

2005

Carandini, How do we look?, The Scientist.

Bonin, Mante, and Carandini, The suppressive field of neurons in lateral geniculate nucleus, J Neurosci.

Mante, Frazor, Bonin, Geisler, and Carandini, Independence of luminance and contrast in natural scenes and in the early visual system, Nature Neuroscience.

Carandini, Demb, Mante, Olshausen, Tolhurst, Dan, Gallant, and Rust Do we know what the early visual system does?, J Neurosci.

Petrov, Carandini, and McKee, Two distinct mechanisms of suppression in human vision. J Neurosci.

Gabernet, Jadhav, Feldman, Carandini, and Scanziani, Somatosensory integration controlled by dynamic thalamocortical feed-forward inhibition, Neuron. [failed cover]. [Code].

Mante and Carandini, Mapping of stimulus energy in primary visual cortex, J Neurophysiol.

2004

Carandini, Amplification of trial-to-trial response variability by neurons in visual cortex PLoS Biology.

Priebe, Mechler, Carandini, and Ferster, The contribution of spike threshold to the dichotomy of cortical simple and complex cells, Nature Neuroscience.

Carandini and Sengpiel, Contrast invariance of functional maps in cat primary visual cortex, J of Vision.

Carandini, Receptive fields and suppressive fields in the early visual system. In The Cognitive Neurosciences, 3d ed., Gazzaniga, ed., MIT Press.

Bonin, Mante, and Carandini, Nonlinear processing in LGN neurons. In Advances in Neural Information Processing Systems 16, Thrun, Saul, and Schölkopf, eds., MIT Press.

2003

Mante and Carandini, Visual cortex: seeing motion, Current Biology.

2002

Carandini, Heeger, and Senn, A synaptic explanation of suppression in visual cortex [Appendix], J Neurosci.

Freeman, Durand, Kiper and Carandini, Suppression without inhibition in visual cortex, Neuron. [failed cover].

Hürlimann, Kiper, and Carandini, Testing the Bayesian model of motion perception, Vision Research.

Meier and Carandini, Masking by fast gratings, J of Vision.

Kiper and Carandini, Neural basis of pattern vision, Encyclopedia of Cognitive Science, MacMillan.

2000

Carandini and Ferster, Membrane potential and firing rate in cat primary visual cortex, J Neurosci.

Anderson, Carandini, and Ferster, Orientation tuning of input conductance, excitation and inhibition in cat primary visual cortex, J Neurophysiol.

Anderson, Lampl, Reichova, Carandini, and Ferster, Stimulus dependence of two-state fluctuations of membrane potential in cat visual cortex, Nature Neuroscience.

Carandini, Visual cortex: fatigue and adaptation, Current Biology.

1999

Carandini, Heeger, and Movshon, Linearity and gain control in V1 simple cells, in Cerebral Cortex. Vol. 13: Models of cortical circuits, Ulinski, Jones and Peters (Eds.), Plenum.

1998

Carandini, Movshon, and Ferster, Pattern adaptation and cross-orientation interactions in the primary visual cortex, Neuropharmacology.

1997

Carandini, Heeger, and Movshon, Linearity and normalization in simple cells of the macaque primary visual cortex, J Neurosci.

Carandini and Ringach, Predictions of a recurrent model of orientation selectivity [code], Vision Research.

Carandini, Barlow, Poirson, O'Keefe, and Movshon, Adaptation to contingencies in macaque primary visual cortex, Phil Trans R Soc London, B.

Carandini and Ferster, A tonic hyperpolarization underlying contrast adaptation in the visual cortex, Science.

1996

Carandini, Mechler, Leonard, and Movshon, Spike train encoding by regular-spiking cells of the visual cortex, J Neurophysiol.

Carandini, Linearity, gain control, and spike encoding in the primary visual cortex, PhD Thesis, New York University.

1995

Carandini and Heeger, Summation and division in V1 simple cells, in The Neurobiology of Computation, Bower (Ed.), Kluwer.

1994

Carandini and Heeger, Summation and division by neurons in visual cortex, Science.

Gegenfurtner, Kiper, Beusmans, Carandini, Zaidi, and Movshon, Chromatic properties of neurons in macaque MT, Visual Neuroscience.