The Arabzadeh Group - Neural Coding

A principal goal of systems neuroscience is to quantify brain activity underlying the complex adaptive behaviour of organisms. We study sensory processing at the level of single cells, circuits and brain pathways. How do single neurons and neuronal populations encode different stimuli? How does the brain ignore less relevant stimulus features and focus on those that are informative to a behavioural task? The Neural Coding Group has a broad interest in systems neuroscience spanning areas such as sensory coding, adaptation and behaviour. We perform neuronal recording from cortex and deep brain structures in anaesthetised as well as awake behaving rodents, and apply methods such as information theory to quantify the way by which single neurons or neuronal ensembles code for sensory stimuli or for the animal's behaviour.

The rat whisker-barrel pathway is our model system of choice. It is also the rat's sensory system of choice for exploring the environment and collecting information about the location, shape, size and texture of objects around it (Diamond & Arabzadeh, 2012). The system is well suited to examining neural coding issues because of its functional efficiency and its elegant structural organisation. The whisker area of somatosensory cortex (known as barrel cortex) is arranged as a topographic map of the whiskers (Woolsey and Van der Loos, 1970; Welker 1971). This means that sensory signals arising in one whisker are channelled through a restricted population of neurons and can be characterised by recording electrodes or through optical imaging.

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Kheradpezhouh E, Mishra W, Arabzadeh E. (2021) A protocol for simultaneous in vivo juxtacellular electrophysiology and local pharmacological manipulation in mouse cortex. STAR Protoc. 2(1):100317. doi: 10.1016/j.xpro.2021.100317. eCollection 2021 Mar 19.

Ghazvineh S, Salimi M, Nazari M, Garousi M, Tabasi F, Dehdar K, Salimi A, Jamaati H, Mirnajafi-Zadeh J, Arabzadeh E, Raoufy MR (2021) Rhythmic air-puff into nasal cavity modulates activity across multiple brain areas: A non-invasive brain stimulation method to reduce ventilator-induced memory impairment. Respir Physiol Neurobiol. 287:103627. doi: 10.1016/j.resp.2021.103627.

Lee CCY, Kheradpezhouh E, Diamond ME, Arabzadeh E. (2020) State-dependent changes in perception and coding in the mouse somatosensory cortex Cell Reports, 32 (13), 108197.

Kheradpezhouh E, Tang MF, Mattingley JB, Arabzadeh E. (2020) Enhanced Sensory Coding in Mouse Vibrissal and Visual Cortex through TRPA1. Cell Reports 32(3):107935.

Gharaei S, Honnuraiah S, Arabzadeh E*, Stuart GJ* (2020) Superior colliculus modulates cortical coding of somatosensory information. Nat Commun. 11(1):1693. doi: 10.1038/s41467-020-15443-1. *co-last author

Tang MF, Ford L, Arabzadeh E, Enns JT, Visser TAW, Mattingley JB (2020) Neural dynamics of the attentional blink revealed by encoding orientation selectivity during rapid visual presentation. Nat Commun. 11(1):434. doi: 10.1038/s41467-019-14107-z.

Dell KL, Arabzadeh E, Price NSC (2019) Differences in perceptual masking between humans and rats. Brain Behav. 9(9):e01368. doi: 10.1002/brb3.1368. Epub 2019 Aug 24.

Ranjbar-Slamloo Y, Arabzadeh E (2019) Diverse tuning underlies sparse activity in L2/3 vibrissal cortex of awake mice J Physiol. 597(10):2803-2817. doi: 10.1113/JP277506.

Lee CCY, Clifford CWG, Arabzadeh E (2019) Temporal cueing enhances neuronal and behavioral discrimination performance in rat whisker system Journal of Neurophysiology, doi: 10.1152/jn.00604.2018

Tang MF, Smout CA, Arabzadeh E, Mattingley JB (2018) Prediction error and repetition suppression have distinct effects on neural representations of visual information  eLife, 7:e33123 DOI: 10.7554/eLife.33123

Gharaei S, Arabzadeh E, Solomon SG (2018) Integration of visual and whisker signals in rat superior colliculus Scientific Reports, 6;8(1):16445. doi: 10.1038/s41598-018-34661-8.

Dell KL, Arabzadeh E, Price NSC. (2018) Human-like perceptual masking is difficult to observe in rats performing an orientation discrimination task. PLoS One. e0207179. doi: 10.1371/journal.pone.0207179.

Sabri MM, Arabzadeh E (2018) Information processing across behavioral states: modes of operation and  population dynamics in rodent sensory cortex. Neuroscience. 368:214-228 Invited review in Barrel cortex issue. doi: 10.1016/j.neuroscience.2017.09.016.

Kheradpezhouh E, Choy JMC, Daria VR, Arabzadeh E (2017) TRPA1 expression and its functional activation in rodent cortex. Open Biology 7(4). pii: 160314. doi: 10.1098/rsob.160314.

Kheradpezhouh E, Adibi M, Arabzadeh E (2017) Response dynamics of rat barrel cortex neurons to repeated sensory stimulation. Scientific Reports 7(1):11445. doi: 10.1038/s41598-017-11477-6.

Ranjbar-Slamloo Y, Arabzadeh E (2017) High-velocity stimulation evokes "dense" population response in layer 2/3 vibrissal cortex. Journal of Neurophysiology 117(3):1218-1228. doi: 10.1152/jn.00815.2016.

Sabri M, Adibi M and Arabzadeh E (2016) Dynamics of population activity in rat sensory cortex: network correlations predict anatomical arrangement and information content. Front. Neural Circuits, 10:49

Lee C, Diamond ME, Arabzadeh E (2016)  Sensory prioritization in rats: behavioural performance and neuronal correlates  Journal of Neuroscience, 36(11): 3243-3253.

Fazlali Z, Ranjbar-Slamloo Y, Adibi M and Arabzadeh E (2016)  Correlation between Cortical State and Locus Coeruleus: Implications for Sensory Coding in Rat Barrel Cortex.  Front. Neural Circuits 10:14

Fam J, Westbrook RF, Arabzadeh E (2016) Temporal dynamics of choice behavior in rats and humans: an examination of pre- and post-choice latencies. Scientific Reports, 6:20583

Fam J, Westbrook RF, Arabzadeh E (2015) Behavioral correlates of the decision process in a dynamic environment: post-choice latencies reflect relative value and choice evaluation. Frontiers in Behavioral Neuroscience, 9:261.

Abrahamyan A, Clifford CWG, Arabzadeh E, Harris JA (2015) Low intensity TMS enhances perception of visual stimuli Brain Stimulation, doi:10.1016/j.brs.2015.06.012

Fam J, Westbrook RF, Arabzadeh E (2015) Dynamics of pre- and post-choice behaviour: rats approximate optimal strategy in a discrete-trial decision task Proceedings of the Royal Society B, 282: 20142963.

McDonald JS, Adibi M, Clifford CWG, Arabzadeh E (2014)  Sampling time and performance in rat whisker system PLoS ONE, 9(12): e116357

Arabzadeh E, Clifford CWG, Harris JA, Mahns DA, Macefield VG, Birznieks I (2014) Single Tactile Afferents Outperform Human Subjects in a Vibrotactile Intensity Discrimination Task. Journal of Neurophysiology, 112: 2382-2387

Adibi M, McDonald JS, Clifford CWG, Arabzadeh E (2014) Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses PLoS Computational Biology, 10(1): e1003415

Adibi M, Clifford CWG, Arabzadeh E (2013)  Informational basis of sensory adaptation: entropy and single spike efficiency in rat barrel cortex  Journal of Neuroscience 33(37): 14921-6

Diamond ME, Arabzadeh E *(2013)  Whisker sensory system – from receptor to decision Progress in Neurobiology 103: 28-40

Adibi M, McDonald JS, Clifford CWG, Arabzadeh E (2013)  Adaptation improves neuronal coding efficiency despite increasing correlations in variability.  Journal of Neuroscience 33(5): 2108-2120

Adibi M, Diamond ME, Arabzadeh E (2012) Behavioral study of whisker-mediated vibration sensation in rats Proceedings of the National Academy of Sciences USA 109(3): 971-6.

Lavan D, McDonald JS, Westbrook RF, Arabzadeh E (2011)  Behavioural Correlate of Choice Confidence in a Discrete Trial Paradigm PLoS ONE 6(10): e26863.

Abrahamyan A, Clifford CW, Ruzzoli M, Phillips D, Arabzadeh E, Harris JA (2011)  Accurate and rapid estimation of phosphene thresholds PLoS ONE 6(7): e22342.

Adibi M, Arabzadeh E (2011) A comparison of neuronal and behavioral performances in rat whisker system Journal of Neurophysiology 105(1): 356-65

Abrahamyan A, Clifford CW, Arabzadeh E, Harris JA (2011)  Improving visual sensitivity with subthreshold transcranial magnetic stimulation Journal of Neuroscience 31(9): 3290-4

Ince RA, Senatore R, Arabzadeh E, Montani F, Diamond ME, Panzeri S. (2010) Information-theoretic methods for studying population codes Neural Network 23(6): 713-27

Lak A, Arabzadeh E, Harris JA, Diamond ME. (2010) Correlated physiological and perceptual effects of noise in a tactile stimulus Proceedings of the National Academy of Sciences USA 107(17): 7981-6

Arabzadeh E, von Heimendahl M, Diamond ME (2009)  Vibrissal texture decoding Scholarpedia 4(4): 6640

Ince RAA, Montani F, Arabzadeh E, Diamond ME, Panzeri S (2009)  On the presence of high-order interactions among somatosensory neurons  Journal of Physics conference series 197 012013 

Montani F, Ince RAA, Senatore R, Arabzadeh E, Diamond ME, Panzeri S (2009) The impact of high-order interactions on the rate of synchronous discharge and information transmission  Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 367 (1901), 3297-3310

Diamond, ME, von Heimendahl, M, Itskov, P, Arabzadeh, E (2008)  Response to: "Embodied Information Processing: Vibrissa Mechanics and Texture Features Shape Micromotions in Actively Sensing Rats."   Neuron 60(5), 743-744

Diamond ME, von Heimendahl M, Arabzadeh E (2008)  Whisker-Mediated Texture Discrimination  PLoS Biology 6(8): e220

Arabzadeh E, Clifford CWG, Harris JA (2008) Vision merges with touch in a purely tactile discrimination.  Psychological Science 19: 635-41

Clifford CWG, Arabzadeh E, Harris JA (2008) A good bet to measure awareness?  Trends in Cognitive Sciences 12: 210  

Clifford CWG, Arabzadeh E, Harris JA (2008) Getting technical about awareness  Trends in Cognitive Sciences 12: 54-8  

Mitchinson B, Arabzadeh E, Diamond ME, Prescott TJ (2008) Spike-timing in primary sensory neurons: A model of somatosensory transduction in the rat Biological Cybernetics 98: 185-94

Lak A, Arabzadeh E, Diamond ME (2008) Retuning of Neuronal Response to Stimuli Containing Temporal Noise in Rat Barrel Cortex  Cerebral Cortex 18: 1085-93

von Heimendahl M, Itskov PM, Arabzadeh E, Diamond ME (2007)  Neuronal Activity in Rat Barrel Cortex Underlying Texture Discrimination PLoS Biology e305

Harris JA, Arabzadeh E, Moore CA, Clifford CWG (2007) Noninformative vision causes adaptive changes in tactile sensitivity. Journal of Neuroscience 27(28)

Maravall M, Petersen RS, Fairhall AL, Arabzadeh E, Diamond ME (2007) Shifts in coding properties and maintenance of information transmission during adaptation in barrel cortex  PLoS Biology 5(2): e19

Arabzadeh E, Panzeri S, Diamond ME (2006) Deciphering the spike train of a sensory neuron: counts and temporal patterns in the rat whisker pathway Journal of Neuroscience 26(36): 9216-26

Harris JA, Arabzadeh E, Fairhall AL, Benito C, Diamond ME (2006) Factors affecting frequency discrimination of vibrotactile stimuli: implications for cortical encoding PLoS ONE 1: e100

Hipp J, Arabzadeh E, Zorzin E, Conradt J, Kayser C, Diamond ME, Konig P (2006) Texture signals in whisker vibrations Journal of Neurophysiology 95(3): 1792-9

Arabzadeh E, Zorzin E, Diamond ME (2005) Neuronal encoding of texture in the whisker pathway. PLoS Biology 3(1): e17

Arabzadeh E, Panzeri S, Diamond ME (2004) Whisker vibration information carried by rat barrel cortex Journal of Neuroscience 24(26): 6011-6020

Arabzadeh E, Petersen RS, Diamond ME (2003)  Encoding of whisker vibration by rat barrel cortex neurons: implications for texture discrimination. Journal of Neuroscience 23(27): 9146-54.


Ehsan Arabzadeh (2010) Neuronal Encoding of Texture in Rat Whisker System spike times and temporal patterns VDM Verlag Germany

Book chapters

S Gharaei, GJ Stuart, E Arabzadeh (2020) Collicular Anatomy and Function In: The senses: A Comprehensive Reference, Second Edition, pp. 549–566. Elsevier.

Arabzadeh E, von Heimendahl M, Diamond ME (2015) Vibrissal texture coding In: Scholarpedia of Touch Editors: Prescott TJ, Ahissar E, Izhikevich E Atlantis Press, Paris

Diamond ME, Arabzadeh E (2013) Coding in the Whisker Sensory System In: Principles of Neural Coding  Editors: Rodrigo Quian Quiroga and Stefano Panzeri

Clifford CWG, Harris JA, Arabzadeh E (2010) Operating characteristics and awareness
In: New Horizons in the Neuroscience of Consciousness  Editors: Perry, Elaine, Daniel Collerton, Fiona E.N. LeBeau and Heather Ashton

Diamond M E, Zorzin E, Arabzadeh E (2005) Neuronal encoding of natural stimuli: the rat tactile system.  In: Percept, Decision, Action: Bridging the Gaps  Editor: Chadwick D,  John Wiley and Sons, Chichester, UK