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{tip:title=Mendeley!}We are maintaining the live 'official' list of ScanImage & Ephus citing/using papers on [Mendeley|http://www.mendeley.com/groups/1607163/scanimage-ephus/papers/]. Periodically we reproduce a snapshot of that list below. You may [join Mendeley|http://www.mendeley.com/] and then [_follow_ the ScanImage & Ephus group|http://www.mendeley.com/groups/1607163/scanimage-ephus/papers/] to be able to search the papers in the group, using either the web client or the [desktop client|http://www.mendeley.com/download-mendeley-desktop/?_section=footer].{tip}

{tip:title=Be Counted!}If you don't see on the list below a paper you've written, or know of, that uses ScanImage and/or Ephus, please [contact us\!|mailto:iyerv@janelia.hhmi.org?subject=\[ScanImage/Ephus Pubs\]] Note you can search the text below using your web browser's Find feature, e.g. Ctrl+F.{tip}

{show-to:groups=ephus-developers}
{note:title=How to Snapshot}
* Set Citation Style to CurrentAmerican Medical OpinionAssociation journals
* Select all documents in Mendeley
* Copy & paste into Word; remove bold
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_Snapshot: 2013-03-11_
Current total primary research publications: *222*
!PubsByYear_2013_03_11.jpg|height=400px!

1. Marvin JS, Borghuis BG, Tian L, et al. An optimized fluorescent probe for visualizing glutamate neurotransmission. _Nature methods_. 2013;10(2):162-70.

2. Beier KT, Borghuis BG, El-Danaf RN, et al. Transsynaptic tracing with vesicular stomatitis virus reveals novel retinal circuitry. _Journal of Neuroscience_. 2013;33(1):35-51.

3. Mostany R, Anstey JE, Crump KL, et al. Altered Synaptic Dynamics during Normal Brain Aging. _Journal of Neuroscience_. 2013;33(9):4094-4104.

4. Horton NG, Wang K, Kobat D, et al. In vivo three-photon microscopy of subcortical structures within an intact mouse brain. _Nature Photonics_. 2013;7(3):205-209.

5. Petreanu L, Gutnisky DA, Huber D, et al. Activity in motor-sensory projections reveals distributed coding in somatosensation. _Nature_. 2012;489(7415):299-303.

6. Xiong Q, Oviedo HV, Trotman LC, Zador AM. PTEN Regulation of Local and Long-Range Connections in Mouse Auditory Cortex. _Journal of Neuroscience_. 2012;32(5):1643-1652.

7. Wu X, Fu Y, Knott G, et al. GABA Signaling Promotes Synapse Elimination and Axon Pruning in Developing Cortical Inhibitory Interneurons. _Journal of Neuroscience_. 2012;32(1):331-43.

8. Jacob V, Petreanu L, Wright N, Svoboda K, Fox K. Regular spiking and intrinsic bursting pyramidal cells show orthogonal forms of experience-dependent plasticity in layer v of barrel cortex. _Neuron_. 2012;73(2):391-404.

9. Seemann KM, Kiefersauer R, Jacob U, Kuhn B. Optical pH detection within a protein crystal. _The journal of physical chemistry. B_. 2012;116(33):9873-81.

10. Viswanathan S, Bandyopadhyay S, Kao JPY, Kanold PO. Changing Microcircuits in the Subplate of the Developing Cortex. _Journal of Neuroscience_. 2012;32(5):1589-1601.

11. Zariwala HA, Borghuis BG, Hoogland TM, et al. A Cre-Dependent GCaMP3 Reporter Mouse for Neuronal Imaging In Vivo. _Journal of Neuroscience_. 2012;32(9):3131-3141.

12. Akerboom J, Chen T-W, Wardill TJ, et al. Optimization of a GCaMP calcium indicator for neural activity imaging. _Journal of Neuroscience_. 2012;32(40):13819-40.

13. Ertürk A, Mauch CP, Hellal F, et al. Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. _Nature medicine_. 2012;18(1):166-71.

14. Arttamangkul S, Lau EK, Lu H-W, Williams JT. Desensitization and Trafficking of mu-opioid Receptors in Locus Coeruleus Neurons: Modulation by Kinases. _Molecular pharmacology_. 2012;81(3):348-55.

15. Atallah BVV, Bruns W, Carandini M, Scanziani M. Parvalbumin-Expressing Interneurons Linearly Transform Cortical Responses to Visual Stimuli. _Neuron_. 2012;73(1):159-170.

16. Packer AM, Peterka DS, Hirtz JJ, et al. Two-photon optogenetics of dendritic spines and neural circuits. _Nature Methods_. 2012;9(12):1202-5.

17. Kuhn B, Ozden I, Lampi Y, Hasan MT, Wang SS-H. An amplified promoter system for targeted expression of calcium indicator proteins in the cerebellar cortex. _Frontiers in neural circuits_. 2012;6:49.

18. Wilson NR, Runyan CA, Wang FL, Sur M. Division and subtraction by distinct cortical inhibitory networks in vivo. _Nature_. 2012;488(7411):343-8.

19. Apicella AJ, Wickersham IR, Seung HS, Shepherd GMG. Laminarly orthogonal excitation of fast-spiking and low-threshold-spiking interneurons in mouse motor cortex. _Journal of Neuroscience_. 2012;32(20):7021-33.

20. Suter BA, Migliore M, Shepherd GMG. Intrinsic Electrophysiology of Mouse Corticospinal Neurons: a Class-Specific Triad of Spike-Related Properties. _Cerebral cortex (New York, N.Y.?: 1991)_. 2012.

21. Kiritani T, Wickersham IR, Seung HS, Shepherd GMG. Hierarchical connectivity and connection-specific dynamics in the corticospinal-corticostriatal microcircuit in mouse motor cortex. _Journal of Neuroscience_. 2012;32(14):4992-5001.

22. Scott BB, Gardner T, Ji N, Fee MS, Lois C. Wandering Neuronal Migration in the Postnatal Vertebrate Forebrain. _Journal of Neuroscience_. 2012;32(4):1436-1446.

23. Odermatt B, Nikolaev A, Lagnado L. Encoding of Luminance and Contrast by Linear and Nonlinear Synapses in the Retina. _Neuron_. 2012;73(4):758-773.

24. Li Y, Lu H, Cheng P-lin, et al. Clonally related visual cortical neurons show similar stimulus feature selectivity. _Nature_. 2012;advance on.

25. Li Y-T, Ma W-P, Pan C-J, Zhang LI, Tao HW. Broadening of Cortical Inhibition Mediates Developmental Sharpening of Orientation Selectivity. _Journal of Neuroscience_. 2012;32(12):3981-3991.

26. Huber D, Gutnisky DA, Peron S, et al. Multiple dynamic representations in the motor cortex during sensorimotor learning. _Nature_. 2012;484(7395):473-478.

27. Xu N-long, Harnett MT, Williams SR, et al. Nonlinear dendritic integration of sensory and motor input during an active sensing task. _Nature_. 2012;492(7428):247-51.

28. Johnston DG, Denizet M, Mostany R, Portera-Cailliau C. Chronic In Vivo Imaging Shows No Evidence of Dendritic Plasticity or Functional Remapping in the Contralesional Cortex after Stroke. _Cerebral cortex (New York, N.Y.?: 1991)_. 2012.

29. Andermann ML, Kerlin AM, Roumis DK, Glickfeld LL, Reid RC. Functional Specialization of Mouse Higher Visual Cortical Areas. _Neuron_. 2011;72(6):1025-1039.

30. Bégin S, Burgoyne B, Mercier V, et al. Coherent anti-Stokes Raman scattering hyperspectral tissue imaging with a wavelength-swept system. _Biomedical optics express_. 2011;2(5):1296-306.

31. Hooks BM, Hires SA, Zhang Y-X, et al. Laminar analysis of excitatory local circuits in vibrissal motor and sensory cortical areas. _PLoS biology_. 2011;9(1):e1000572.

32. Lam Y-W, Sherman SM. Functional organization of the thalamic input to the thalamic reticular nucleus. _Journal of Neuroscience_. 2011;31(18):6791-9.

33. Peñagarikano O, Abrahams BS, Herman EI, et al. Absence of CNTNAP2 Leads to Epilepsy, Neuronal Migration Abnormalities, and Core Autism-Related Deficits. _Cell_. 2011;147(1):235-246.

34. Ramsey AJ, Milenkovic M, Oliveira AF, et al. Impaired NMDA receptor transmission alters striatal synapses and DISC1 protein in an age-dependent manner. _Proceedings of the National Academy of Sciences_. 2011;108(14):5795.

35. Rosselet C, Fieschi M, Hugues S, Bureau I. Associative learning changes the organization of functional excitatory circuits targeting the supragranular layers of mouse barrel cortex. _Frontiers in neural circuits_. 2011;4:126.

36. Middleton JW, Kiritani T, Pedersen C, et al. Mice with behavioral evidence of tinnitus exhibit dorsal cochlear nucleus hyperactivity because of decreased GABAergic inhibition. _Proceedings of the National Academy of Sciences_. 2011;108(18):7601-6.

37. Lien AD, Scanziani M. In vivo Labeling of Constellations of Functionally Identified Neurons for Targeted in vitro Recordings. _Frontiers in neural circuits_. 2011;5:16.

38. Viaene AN, Petrof I, Sherman SM. Synaptic properties of thalamic input to layers 2/3 and 4 of primary somatosensory and auditory cortices. _Journal of neurophysiology_. 2011;105(1):279-92.

39. Mao T, Kusefoglu D, Hooks BM, et al. Long-Range Neuronal Circuits Underlying the Interaction between Sensory and Motor Cortex. _Neuron_. 2011;72(1):111-123.

40. Baden T, Esposti F, Nikolaev A, Lagnado L. Spikes in Retinal Bipolar Cells Phase-Lock to Visual Stimuli with Millisecond Precision. _Current biology_. 2011;21(22):1859-69.

41. Sheets PL, Suter BA, Kiritani T, et al. Corticospinal-specific HCN expression in mouse motor cortex: I(h)-dependent synaptic integration as a candidate microcircuit mechanism involved in motor control. _Journal of neurophysiology_. 2011;106(5):2216-31.

42. Miri A, Daie K, Arrenberg AB, et al. Spatial gradients and multidimensional dynamics in a neural integrator circuit. _Nature Neuroscience_. 2011;14(9):1150-9.

43. Blumhagen F, Zhu P, Shum J, et al. Neuronal filtering of multiplexed odour representations. _Nature_. 2011;479(7374):493-498.

44. Pugh JR, Jahr CE. Axonal GABAA receptors increase cerebellar granule cell excitability and synaptic activity. _Journal of Neuroscience_. 2011;31(2):565-74.

45. Tuthill JC, Chiappe ME, Reiser MB. Neural correlates of illusory motion perception in Drosophila. _Proceedings of the National Academy of Sciences of the United States of America_. 2011;108(23):9685-90.

46. Chalifoux JR, Carter AG. GABAB receptor modulation of voltage-sensitive calcium channels in spines and dendrites. _The Journal of Neuroscience_. 2011;31(11):4221-32.

47. Berndt A, Schoenenberger P, Mattis J, et al. High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels. _Proceedings of the National Academy of Sciences of the United States of America_. 2011;108(18):7595-600.

48. Dreosti E, Esposti F, Baden T, Lagnado L. In vivo evidence that retinal bipolar cells generate spikes modulated by light. _Nature neuroscience_. 2011;14(8):951-2.

49. Bock DD, Lee W-CA, Kerlin AM, et al. Network anatomy and in vivo physiology of visual cortical neurons. _Nature_. 2011;471(7337):177-82.

50. Kitamura K, Hausser M. Dendritic Calcium Signaling Triggered by Spontaneous and Sensory-Evoked Climbing Fiber Input to Cerebellar Purkinje Cells In Vivo. _Journal of Neuroscience_. 2011;31(30):10847-10858.

51. Mostany R, Portera-Cailliau C. Absence of large-scale dendritic plasticity of layer 5 pyramidal neurons in peri-infarct cortex. _Journal of Neuroscience_. 2011;31(5):1734-8.

52. Herman MA, Nahir B, Jahr CE. Distribution of extracellular glutamate in the neuropil of hippocampus. _PloS one_. 2011;6(11):e26501.

53. Qiu S, Anderson CT, Levitt P, Shepherd GMG. Circuit-specific intracortical hyperconnectivity in mice with deletion of the autism-associated Met receptor tyrosine kinase. _Journal of Neuroscience_. 2011;31(15):5855-64.

54. Ikrar T, Olivas ND, Shi Y, Xu X. Mapping inhibitory neuronal circuits by laser scanning photostimulation. _Journal of visualized experiments?: JoVE_. 2011;(56).

55. Miri A, Daie K, Burdine RD, Aksay E, Tank DW. Regression-based identification of behavior-encoding neurons during large-scale optical imaging of neural activity at cellular resolution. _Journal of neurophysiology_. 2011;105(2):964-80.

56. Marshel JH, Garrett ME, Nauhaus I, Callaway EM. Functional Specialization of Seven Mouse Visual Cortical Areas. _Neuron_. 2011;72(6):1040-1054.

57. Pugh JR, Jahr CE. NMDA Receptor Agonists Fail To Alter Release from Cerebellar Basket Cells. _Journal of Neuroscience_. 2011;31(46):16550-16555.

58. Acker CD, Yan P, Loew LM. Single-voxel recording of voltage transients in dendritic spines. _Biophysical journal_. 2011;101(2):L11-3.

59. Truong TV, Supatto W, Koos DS, Choi JM, Fraser SE. Deep and fast live imaging with two-photon scanned light-sheet microscopy. _Nature Methods_. 2011;8(9):757-60.

60. Kuhlman SJ, Tring E, Trachtenberg JT. Fast-spiking interneurons have an initial orientation bias that is lost with vision. _Nature neuroscience_. 2011;14(9):1121-3.

61. Christie JM, Chiu DN, Jahr CE. Ca(2+)-dependent enhancement of release by subthreshold somatic depolarization. _Nature neuroscience_. 2011;14(1):62-8.

62. Viaene AN, Petrof I, Sherman SM. Properties of the thalamic projection from the posterior medial nucleus to primary and secondary somatosensory cortices in the mouse. _Proceedings of the National Academy of Sciences_. 2011;108(44):18156-61.

63. Lewis TL, Mao T, Arnold DB. A role for myosin VI in the localization of axonal proteins. _PLoS biology_. 2011;9(3):e1001021.

64. Mellios N, Sugihara H, Castro J, et al. miR-132, an experience-dependent microRNA, is essential for visual cortex plasticity. _Nature neuroscience_. 2011;14(10):1240-2.

65. Mostaço-Guidolin LB, Ko AC-T, Popescu DP, et al. Evaluation of texture parameters for the quantitative description of multimodal nonlinear optical images from atherosclerotic rabbit arteries. _Physics in medicine and biology_. 2011;56(16):5319-34.

66. Woods GF, Oh WC, Boudewyn LC, Mikula SK, Zito K. Loss of PSD-95 Enrichment Is Not a Prerequisite for Spine Retraction. _Journal of Neuroscience_. 2011;31(34):12129-12138.

67. Viaene AN, Petrof I, Sherman SM. Synaptic Properties of Thalamic Input to the Subgranular Layers of Primary Somatosensory and Auditory Cortices in the Mouse. _Journal of Neuroscience_. 2011;31(36):12738-12747.

68. Borghuis BG, Tian L, Xu Y, et al. Imaging light responses of targeted neuron populations in the rodent retina. _Journal of Neuroscience_. 2011;31(8):2855-67.

69. Quillinan N, Lau EK, Virk M, von Zastrow M, Williams JT. Recovery from mu-opioid receptor desensitization after chronic treatment with morphine and methadone. _Journal of Neuroscience_. 2011;31(12):4434-43.

70. Nauhaus I, Nielsen KJ, Callaway EM. Nonlinearity of two-photon Ca2\+ imaging yields distorted measurements of tuning for V1 neuronal populations. _Journal of neurophysiology_. 2011;107(3):923-36.

71. Sedlacek M, Tipton PW, Brenowitz SD. Sustained firing of cartwheel cells in the dorsal cochlear nucleus evokes endocannabinoid release and retrograde suppression of parallel fiber synapses. _Journal of Neuroscience_. 2011;31(44):15807-17.

72. Hamad MIK, Ma-Högemeier Z-L, Riedel C, et al. Cell class-specific regulation of neocortical dendrite and spine growth by AMPA receptor splice and editing variants. _Development_. 2011;138(19):4301-13.

73. De Pasquale R, Sherman SM. Synaptic Properties of Corticocortical Connections between the Primary and Secondary Visual Cortical Areas in the Mouse. _Journal of Neuroscience_. 2011;31(46):16494-16506.

74. Herzog E, Nadrigny F, Silm K, et al. In Vivo Imaging of Intersynaptic Vesicle Exchange Using VGLUT1Venus Knock-In Mice. _Journal of Neuroscience_. 2011;31(43):15544-15559.

75. Liu CC, Gao SS, Yuan T, et al. Biophysical mechanisms underlying outer hair cell loss associated with a shortened tectorial membrane. _Journal of the Association for Research in Otolaryngology?: JARO_. 2011;12(5):577-94.

76. Chalifoux JR, Carter AG. Glutamate Spillover Promotes the Generation of NMDA Spikes. _Journal of Neuroscience_. 2011;31(45):16435-16446.

77. Vesuna S, Torres R, Levene MJ. Multiphoton fluorescence, second harmonic generation, and fluorescence lifetime imaging of whole cleared mouse organs. _Journal of biomedical optics_. 2011;16(10):106009.

78. Ma W-P, Liu B-H, Li Y-T, et al. Visual representations by cortical somatostatin inhibitory neurons--selective but with weak and delayed responses. _Journal of Neuroscience_. 2010;30(43):14371-9.

79. Komiyama T, Sato TR, O'Connor DH, et al. Learning-related fine-scale specificity imaged in motor cortex circuits of behaving mice. _Nature_. 2010;464(7292):1182-6.

80. Seelig JD, Chiappe ME, Lott GK, et al. Two-photon calcium imaging from head-fixed Drosophila during optomotor walking behavior. _Nature methods_. 2010;7(7):535-40.

81. Chowdhury TG, Jimenez JC, Bomar JM, et al. Fate of cajal-retzius neurons in the postnatal mouse neocortex. _Frontiers in neuroanatomy_. 2010;4:10.

82. Cruz-Martín A, Crespo M, Portera-Cailliau C. Delayed stabilization of dendritic spines in fragile X mice. _The Journal of Neuroscience_. 2010;30(23):7793-803.

83. Higley MJ, Sabatini BL. Competitive regulation of synaptic Ca2\+ influx by D2 dopamine and A2A adenosine receptors. _Nature neuroscience_. 2010;13(8):958-66.

84. Guetg N, Abdel Aziz S, Holbro N, et al. NMDA receptor-dependent GABAB receptor internalization via CaMKII phosphorylation of serine 867 in GABAB1. _Proceedings of the National Academy of Sciences of the United States of America_. 2010;107(31):13924-9.

85. Heider B, Nathanson JL, Isacoff EY, Callaway EM, Siegel RM. Two-Photon Imaging of Calcium in Virally Transfected Striate Cortical Neurons of Behaving Monkey. _PloS one_. 2010;5(11):e13829.

86. Patterson MA, Szatmari EM, Yasuda R. AMPA receptors are exocytosed in stimulated spines and adjacent dendrites in a Ras-ERK-dependent manner during long-term potentiation. _Proceedings of the National Academy of Sciences of the United States of America_. 2010;107(36):15951-6.

87. Wilbrecht L, Holtmaat A, Wright N, Fox K, Svoboda K. Structural plasticity underlies experience-dependent functional plasticity of cortical circuits. _The Journal of Neuroscience_. 2010;30(14):4927-32.

88. Chiappe ME, Seelig JD, Reiser MB, Jayaraman V. Walking modulates speed sensitivity in Drosophila motion vision. _Current biology_. 2010;20(16):1470-5.

89. Xia A, Gao SS, Yuan T, et al. Deficient forward transduction and enhanced reverse transduction in the alpha tectorin C1509G human hearing loss mutation. _Disease models & mechanisms_. 2010;3(3-4):209-23.

90. Chalifoux JR, Carter AG. GABAB receptors modulate NMDA receptor calcium signals in dendritic spines. _Neuron_. 2010;66(1):101-13.

91. Oviedo HV, Bureau I, Svoboda K, Zador AM. The functional asymmetry of auditory cortex is reflected in the organization of local cortical circuits. _Nature neuroscience_. 2010;13(11):1413-20.

92. Mostaço-Guidolin LB, Sowa MG, Ridsdale A, et al. Differentiating atherosclerotic plaque burden in arterial tissues using femtosecond CARS-based multimodal nonlinear optical imaging. _Biomedical optics express_. 2010;1(1):59-73.

93. Theyel BB, Llano DA, Sherman SM. The corticothalamocortical circuit drives higher-order cortex in the mouse. _Nature neuroscience_. 2010;13(1):84-8.

94. Kerlin AM, Andermann ML, Berezovskii VK, Reid RC. Broadly tuned response properties of diverse inhibitory neuron subtypes in mouse visual cortex. _Neuron_. 2010;67(5):858-71.

95. Parra SG, Chia TH, Zinter JP, Levene MJ. Multiphoton microscopy of cleared mouse organs. _Journal of biomedical optics_. 2010;15(3):036017.

96. Lam Y-W, Sherman SM. Functional organization of the somatosensory cortical layer 6 feedback to the thalamus. _Cerebral cortex_. 2010;20(1):13-24.

97. Christie LA, Russell TA, Xu J, et al. AMPA receptor desensitization mutation results in severe developmental phenotypes and early postnatal lethality. _Proceedings of the National Academy of Sciences_. 2010;107(20):9412-7.

98. Shi Y, Nenadic Z, Xu X. Novel use of matched filtering for synaptic event detection and extraction. _PloS one_. 2010;5(11):e15517.

99. Heneka MTM, Nadrigny F, Regen T, et al. Locus ceruleus controls Alzheimer's disease pathology by modulating microglial functions through norepinephrine. _Proceedings of the National Academy of Sciences of the United States of America_. 2010;107(13):6058-63.

100. Anderson CT, Sheets PL, Kiritani T, Shepherd GMG. Sublayer-specific microcircuits of corticospinal and corticostriatal neurons in motor cortex. _Nature neuroscience_. 2010;13(6):739-44.

101. Wiechert MT, Judkewitz B, Riecke H, Friedrich RW. Mechanisms of pattern decorrelation by recurrent neuronal circuits. _Nature neuroscience_. 2010;13(8):1003-10.

102. Dorostkar MMM, Dreosti E, Odermatt B, Lagnado L. Computational processing of optical measurements of neuronal and synaptic activity in networks. _Journal of neuroscience methods_. 2010;188(1):141-50.

103. Ko ACT, Ridsdale A, Smith MSD, et al. Multimodal nonlinear optical imaging of atherosclerotic plaque development in myocardial infarction-prone rabbits. _Journal of biomedical optics_. 2010;15(2):020501.

104. Holbro N, Grunditz A, Wiegert JS, Oertner TG. AMPA receptors gate spine Ca(2+) transients and spike-timing-dependent potentiation. _Proceedings of the National Academy of Sciences_. 2010;107(36):15975-80.

105. Martin SM, O'Brien GS, Portera-Cailliau C, Sagasti A. Wallerian degeneration of zebrafish trigeminal axons in the skin is required for regeneration and developmental pruning. _Development_. 2010;137(23):3985-94.

106. O'Connor DH, Peron SP, Huber D, Svoboda K. Neural activity in barrel cortex underlying vibrissa-based object localization in mice. _Neuron_. 2010;67(6):1048-61.

107. Wood L, Shepherd GMG. Synaptic circuit abnormalities of motor-frontal layer 2/3 pyramidal neurons in a mutant mouse model of Rett syndrome. _Neurobiology of disease_. 2010;38(2):281-7.

108. O'Connor DH, Clack NG, Huber D, et al. Vibrissa-based object localization in head-fixed mice. _Journal of Neuroscience_. 2010;30(5):1947-67.

109. Ch'ng YH, Reid RC. Cellular imaging of visual cortex reveals the spatial and functional organization of spontaneous activity. _Frontiers in integrative neuroscience_. 2010;4.

110. Sato TR, Svoboda K. The functional properties of barrel cortex neurons projecting to the primary motor cortex. _Journal of Neuroscience_. 2010;30(12):4256-60.

111. Dombeck DA, Harvey CD, Tian L, Looger LL, Tank DW. Functional imaging of hippocampal place cells at cellular resolution during virtual navigation. _Nature neuroscience_. 2010;13(11):1433-40.

112. Mostany R, Chowdhury TG, Johnston DG, et al. Local hemodynamics dictate long-term dendritic plasticity in peri-infarct cortex. _Journal of Neuroscience_. 2010;30(42):14116-26.

113. Xu X, Olivas ND, Levi R, Ikrar T, Nenadic Z. High precision and fast functional mapping of cortical circuitry through a novel combination of voltage sensitive dye imaging and laser scanning photostimulation. _Journal of neurophysiology_. 2010;103(4):2301-12.

114. Yuan T, Gao SS, Saggau P, Oghalai JS. Calcium imaging of inner ear hair cells within the cochlear epithelium of mice using two-photon microscopy. _Journal of biomedical optics_. 2010;15(1):016002.

115. Niessing J, Friedrich RW. Olfactory pattern classification by discrete neuronal network states. _Nature_. 2010;465(7294):47-52.

116. Smith SL, Häusser M. Parallel processing of visual space by neighboring neurons in mouse visual cortex. _Nature neuroscience_. 2010;13(9):1144-9.

117. Andermann ML, Kerlin AM, Reid R. Chronic cellular imaging of mouse visual cortex during operant behavior and passive viewing. _Frontiers in Cellular Neuroscience_. 2010;4.

118. Yu YJ, Arttamangkul S, Evans CJ, Williams JT, von Zastrow M. Neurokinin 1 receptors regulate morphine-induced endocytosis and desensitization of mu-opioid receptors in CNS neurons. _Journal of Neuroscience_. 2009;29(1):222-33.

119. Lee CC, Sherman SM. Glutamatergic inhibition in sensory neocortex. _Cerebral cortex_. 2009;19(10):2281-9.

120. Virk MS, Arttamangkul S, Birdsong WT, Williams JT. Buprenorphine is a weak partial agonist that inhibits opioid receptor desensitization. _The Journal of Neuroscience_. 2009;29(22):7341-8.

121. Zito K, Scheuss V, Knott G, Hill T, Svoboda K. Rapid functional maturation of nascent dendritic spines. _Neuron_. 2009;61(2):247--258.

122. Knott GW, Holtmaat A, Trachtenberg JT, Svoboda K, Welker E. A protocol for preparing GFP-labeled neurons previously imaged in vivo and in slice preparations for light and electron microscopic analysis. _Nature protocols_. 2009;4(8):1145-56.

123. Schoenenberger P, Gerosa D, Oertner TG. Temporal control of immediate early gene induction by light. _PLoS One_. 2009;4(12):e8185.

124. Liu B-hua, Li P, Li Y-tang, et al. Visual receptive field structure of cortical inhibitory neurons revealed by two-photon imaging guided recording. _Journal of Neuroscience_. 2009;29(34):10520-32.

125. Judkewitz B, Rizzi M, Kitamura K, Häusser M. Targeted single-cell electroporation of mammalian neurons in vivo. _Nature protocols_. 2009;4(6):862-9.

126. Chia TH, Levene MJ. Microprisms for in vivo multilayer cortical imaging. _Journal of neurophysiology_. 2009;102(2):1310-4.

127. Simons SB, Escobedo Y, Yasuda R, Dudek SM. Regional differences in hippocampal calcium handling provide a cellular mechanism for limiting plasticity. _Proceedings of the National Academy of Sciences of the United States of America_. 2009;106(33):14080-4.

128. Christie JM, Jahr CE. Selective expression of ligand-gated ion channels in L5 pyramidal cell axons. _Journal of Neuroscience_. 2009;29(37):11441.

129. Zhao C, Kao JPY, Kanold PO. Functional excitatory microcircuits in neonatal cortex connect thalamus and layer 4. _Journal of Neuroscience_. 2009;29(49):15479-88.

130. Watt AJ, Cuntz H, Mori M, et al. Traveling waves in developing cerebellar cortex mediated by asymmetrical Purkinje cell connectivity. _Nature neuroscience_. 2009;12(4):463-73.

131. Holtmaat A, Bonhoeffer T, Chow DK, et al. Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window. _Nature protocols_. 2009;4(8):1128-44.

132. Wood L, Gray NW, Zhou Z, Greenberg ME, Shepherd GMG. Synaptic circuit abnormalities of motor-frontal layer 2/3 pyramidal neurons in an RNA interference model of methyl-CpG-binding protein 2 deficiency. _Journal of Neuroscience_. 2009;29(40):12440-8.

133. Petrof I, Sherman SM. Synaptic properties of the mammillary and cortical afferents to the anterodorsal thalamic nucleus in the mouse. _Journal of Neuroscience_. 2009;29(24):7815-9.

134. Golshani P, Gonçalves JT, Khoshkhoo S, et al. Internally mediated developmental desynchronization of neocortical network activity. _Journal of Neuroscience_. 2009;29(35):10890.

135. Holbro N, Grunditz Å, Oertner TG. Differential distribution of endoplasmic reticulum controls metabotropic signaling and plasticity at hippocampal synapses. _Proceedings of the National Academy of Sciences_. 2009;106(35):15055.

136. Ding JB, Takasaki KT, Sabatini BL. Supraresolution imaging in brain slices using stimulated-emission depletion two-photon laser scanning microscopy. _Neuron_. 2009;63(4):429--437.

137. O'Brien G, Rieger S. Two-photon axotomy and time-lapse confocal imaging in live zebrafish embryos. _Journal of visualized experiments?: JoVE_. 2009.

138. Higley MJM, Soler-Llavina GJ, Sabatini BL. Cholinergic modulation of multivesicular release regulates striatal synaptic potency and integration. _Nature neuroscience_. 2009;12(9):1121-8.

139. Lewis TL, Mao T, Svoboda K, Arnold DB. Myosin-dependent targeting of transmembrane proteins to neuronal dendrites. _Nature neuroscience_. 2009;12(5):568-76.

140. Zhong H, Sia GM, Sato TR, et al. Subcellular dynamics of type II PKA in neurons. _Neuron_. 2009;62(3):363--374.

141. Matter C, Pribadi M, Liu X, Trachtenberg JT. Delta-catenin is required for the maintenance of neural structure and function in mature cortex in vivo. _Neuron_. 2009;64(3):320-7.

142. Ozden I, Sullivan MR, Lee HM, Wang SS-H. Reliable coding emerges from coactivation of climbing fibers in microbands of cerebellar Purkinje neurons. _Journal of Neuroscience_. 2009;29(34):10463-73.

143. Chia TH, Levene MJ. In vivo imaging of deep cortical layers using a microprism. _Journal of visualized experiments?: JoVE_. 2009;(30).

144. Llano DA, Sherman SM. Differences in intrinsic properties and local network connectivity of identified layer 5 and layer 6 adult mouse auditory corticothalamic neurons support a dual corticothalamic projection hypothesis. _Cerebral cortex_. 2009;19(12):2810-26.

145. Schultz SR, Kitamura K, Post-Uiterweer A, Krupic J, Häusser M. Spatial pattern coding of sensory information by climbing fiber-evoked calcium signals in networks of neighboring cerebellar Purkinje cells. _The Journal of Neuroscience_. 2009;29(25):8005-15.

146. Hoogland TM, Kuhn B, Göbel W, et al. Radially expanding transglial calcium waves in the intact cerebellum. _Proceedings of the National Academy of Sciences_. 2009;106(9):3496.

147. Tian L, Hires SA, Mao T, et al. Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. _Nature methods_. 2009;6(12):875-81.

148. O'Brien GS, Martin SM, Söllner C, et al. Developmentally regulated impediments to skin reinnervation by injured peripheral sensory axon terminals. _Current biology_. 2009;19(24):2086-90.

149. Dreosti E, Odermatt B, Dorostkar MM, Lagnado L. A genetically encoded reporter of synaptic activity in vivo. _Nature methods_. 2009;6(12):883-9.

150. Dombeck DA, Graziano MS, Tank DW. Functional clustering of neurons in motor cortex determined by cellular resolution imaging in awake behaving mice. _Journal of Neuroscience_. 2009;29(44):13751-60.

151. Petreanu L, Mao T, Sternson SM, Svoboda K. The subcellular organization of neocortical excitatory connections. _Nature_. 2009;457(7233):1142-5.

152. Chow DK, Groszer M, Pribadi M, et al. Laminar and compartmental regulation of dendritic growth in mature cortex. _Nature neuroscience_. 2009;12(2):116-8.

153. Lee CC, Sherman SM. Synaptic properties of thalamic and intracortical inputs to layer 4 of the first\- and higher-order cortical areas in the auditory and somatosensory systems. _Journal of neurophysiology_. 2008;100(1):317-26.

154. Gregor T, McGregor AP, Wieschaus EF. Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. _Developmental biology_. 2008;316(2):350-8.

155. Zhang Y-P, Holbro N, Oertner TG. Optical induction of plasticity at single synapses reveals input-specific accumulation of alphaCaMKII. _Proceedings of the National Academy of Sciences of the United States of America_. 2008;105(33):12039-44.

156. Harvey CD, Yasuda R, Zhong H, Svoboda K. The spread of Ras activity triggered by activation of a single dendritic spine. _Science_. 2008;321(5885):136-40.

157. Cruz-Martín A, Schweizer FE. Imbalance between excitation and inhibition among synaptic connections of CA3 pyramidal neurons in cultured hippocampal slices. _The European journal of neuroscience_. 2008;27(6):1353-63.

158. Bigelow AW, Geard CR, Randers-Pehrson G, Brenner DJ. Microbeam-integrated multiphoton imaging system. _The Review of scientific instruments_. 2008;79(12):123707.

159. Major G, Polsky A, Denk W, Schiller J, Tank DW. Spatiotemporally graded NMDA spike/plateau potentials in basal dendrites of neocortical pyramidal neurons. _Journal of neurophysiology_. 2008;99(5):2584-601.

160. Riegel AC, Williams JT. CRF facilitates calcium release from intracellular stores in midbrain dopamine neurons. _Neuron_. 2008;57(4):559--570.

161. Yu J, Anderson CT, Kiritani T, et al. Local-Circuit Phenotypes of Layer 5 Neurons in Motor-Frontal Cortex of YFP-H Mice. _Frontiers in neural circuits_. 2008;2:6.

162. Grunditz Å, Holbro N, Tian L, Zuo Y, Oertner TG. Spine neck plasticity controls postsynaptic calcium signals through electrical compartmentalization. _Journal of Neuroscience_. 2008;28(50):13457.

163. Kuhlman SJ, Huang ZJ. High-resolution labeling and functional manipulation of specific neuron types in mouse brain by Cre-activated viral gene expression. _PLoS One_. 2008;3(4):e2005.

164. Gandhi SP, Yanagawa Y, Stryker MP. Delayed plasticity of inhibitory neurons in developing visual cortex. _Proceedings of the National Academy of Sciences_. 2008;105(43):16797.

165. Weiler N, Wood L, Yu J, Solla SA, Shepherd GMG. Top-down laminar organization of the excitatory network in motor cortex. _Nature neuroscience_. 2008;11(3):360-6.

166. Kitamura K, Judkewitz B, Kano M, Denk W, Häusser M. Targeted patch-clamp recordings and single-cell electroporation of unlabeled neurons in vivo. _Nature methods_. 2008;5(1):61-7.

167. Atasoy D, Aponte Y, Su HH, Sternson SM. A FLEX switch targets Channelrhodopsin-2 to multiple cell types for imaging and long-range circuit mapping. _Journal of Neuroscience_. 2008;28(28):7025-30.

168. Golshani P, Portera-Cailliau C. In vivo 2-photon calcium imaging in layer 2/3 of mice. _Journal of visualized experiments?: JoVE_. 2008;(13).

169. Mostany R, Portera-Cailliau C. A method for 2-photon imaging of blood flow in the neocortex through a cranial window. _Journal of visualized experiments?: JoVE_. 2008;(12).

170. Arttamangkul S, Quillinan N, Low MJ, et al. Differential activation and trafficking of $\mu$-opioid receptors in brain slices. _Molecular pharmacology_. 2008;74(4):972.

171. Ozden I, Lee HM, Sullivan MR, Wang SS-H. Identification and clustering of event patterns from in vivo multiphoton optical recordings of neuronal ensembles. _Journal of neurophysiology_. 2008;100(1):495-503.

172. Harvey CD, Ehrhardt AG, Cellurale C, et al. A genetically encoded fluorescent sensor of ERK activity. _Proceedings of the National Academy of Sciences_. 2008;105(49):19264.

173. Christie JM, Jahr CE. Dendritic NMDA receptors activate axonal calcium channels. _Neuron_. 2008;60(2):298--307.

174. Mao T, O'Connor DH, Scheuss V, Nakai J, Svoboda K. Characterization and subcellular targeting of GCaMP-type genetically-encoded calcium indicators. _PLoS One_. 2008;3(3):e1796.

175. Bureau I, Shepherd GMG, Svoboda K. Circuit and plasticity defects in the developing somatosensory cortex of FMR1 knock-out mice. _Journal of Neuroscience_. 2008;28(20):5178-88.

176. Sato TR, Gray NW, Mainen ZF, Svoboda K. The functional microarchitecture of the mouse barrel cortex. _PLoS biology_. 2007;5(7):e189.

177. Carter AG, Soler-Llavina GJ, Sabatini BL. Timing and location of synaptic inputs determine modes of subthreshold integration in striatal medium spiny neurons. _Journal of Neuroscience_. 2007;27(33):8967.

178. Gregor T, Tank DW, Wieschaus EF, Bialek W. Probing the limits to positional information. _Cell_. 2007;130(1):153--164.

179. Zhang Y-P, Oertner TG. Optical induction of synaptic plasticity using a light-sensitive channel. _Nature methods_. 2007;4(2):139-41.

180. Dombeck DA, Khabbaz AN, Collman F, Adelman TL, Tank DW. Imaging large-scale neural activity with cellular resolution in awake, mobile mice. _Neuron_. 2007;56(1):43--57.

181. Petreanu L, Huber D, Sobczyk A, Svoboda K. Channelrhodopsin-2-assisted circuit mapping of long-range callosal projections. _Nature neuroscience_. 2007;10(5):663-8.

182. Sjöström PJ, Turrigiano GG, Nelson SB. Multiple forms of long-term plasticity at unitary neocortical layer 5 synapses. _Neuropharmacology_. 2007;52(1):176-84.

183. Huber D, Petreanu L, Ghitani N, et al. Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice. _Nature_. 2007;451(7174):61--64.

184. Lam Y-W, Sherman SM. Different topography of the reticulothalmic inputs to first\- and higher-order somatosensory thalamic relays revealed using photostimulation. _Journal of neurophysiology_. 2007;98(5):2903-9.

185. Harvey CD, Svoboda K. Locally dynamic synaptic learning rules in pyramidal neuron dendrites. _Nature_. 2007;450(7173):1195--1200.

186. Sobczyk A, Svoboda K. Activity-dependent plasticity of the NMDA-receptor fractional Ca2\+ current. _Neuron_. 2007;53(1):17--24.

187. Gregor T, Wieschaus EF, McGregor AP, Bialek W, Tank DW. Stability and nuclear dynamics of the bicoid morphogen gradient. _Cell_. 2007;130(1):141-52.

188. Birbach A, Verkuyl JM, Matus A. Reversible, activity-dependent targeting of profilin to neuronal nuclei. _Experimental cell research_. 2006;312(12):2279-87.

189. Arttamangkul S, Torrecilla M, Kobayashi K, Okano H, Williams JT. Separation of $\mu$-Opioid Receptor Desensitization and Internalization: Endogenous Receptors in Primary Neuronal Cultures. _Journal of Neuroscience_. 2006;26(15):4118.

190. Soler-Llavina GJ, Sabatini BL. Synapse-specific plasticity and compartmentalized signaling in cerebellar stellate cells. _Nature neuroscience_. 2006;9(6):798-806.

191. Papageorgas P, Maroulis D, Anagnostopoulos G, et al. A high-performance imaging and control system for a micromirror-based laser-scanning endoscope device. _IEEE Transactions on Instrumentation and Measurement_. 2006;55(5):1725 - 1733.

192. Vigot R, Barbieri S, Bräuner-Osborne H, et al. Differential compartmentalization and distinct functions of GABAB receptor variants. _Neuron_. 2006;50(4):589--601.

193. Bureau I, von Saint Paul F, Svoboda K. Interdigitated paralemniscal and lemniscal pathways in the mouse barrel cortex. _PLoS biology_. 2006;4(12):e382.

194. Lam Y-W, Nelson CS, Sherman SM. Mapping of the functional interconnections between thalamic reticular neurons using photostimulation. _Journal of neurophysiology_. 2006;96(5):2593-600.

195. Scheuss V, Yasuda R, Sobczyk A, Svoboda K. Nonlinear \[Ca2+\] signaling in dendrites and spines caused by activity-dependent depression of Ca2\+ extrusion. _Journal of Neuroscience_. 2006;26(31):8183.

196. Sjöström PJ, Häusser M. A cooperative switch determines the sign of synaptic plasticity in distal dendrites of neocortical pyramidal neurons. _Neuron_. 2006;51(2):227-38.

197. Holtmaat A, Wilbrecht L, Knott GW, Welker E, Svoboda K. Experience-dependent and cell-type-specific spine growth in the neocortex. _Nature_. 2006;441(7096):979-83.

198. De Paola V, Holtmaat A, Knott G, et al. Cell type-specific structural plasticity of axonal branches and boutons in the adult neocortex. _Neuron_. 2006;49(6):861--875.

199. Knott GW, Holtmaat A, Wilbrecht L, Welker E, Svoboda K. Spine growth precedes synapse formation in the adult neocortex in vivo. _Nature neuroscience_. 2006;9(9):1117-24.

200. Gray NW, Weimer RM, Bureau I, Svoboda K. Rapid redistribution of synaptic PSD-95 in the neocortex in vivo. _PLoS Biology_. 2006;4(11):e370.

201. Yasuda R, Harvey CD, Zhong H, et al. Supersensitive Ras activation in dendrites and spines revealed by two-photon fluorescence lifetime imaging. _Nature neuroscience_. 2006;9(2):283--291.

202. Portera-Cailliau C, Weimer RM, De Paola V, Caroni P, Svoboda K. Diverse modes of axon elaboration in the developing neocortex. _PLoS Biology_. 2005;3(8):e272.

203. Sternson SM, Shepherd GMG, Friedman JM. Topographic mapping of VMH \--> arcuate nucleus microcircuits and their reorganization by fasting. _Nature neuroscience_. 2005;8(10):1356-63.

204. Sobczyk A, Scheuss V, Svoboda K. NMDA receptor subunit-dependent \[Ca2+\] signaling in individual hippocampal dendritic spines. _Journal of Neuroscience_. 2005;25(26):6037.

205. Holtmaat AJGD, Trachtenberg JT, Wilbrecht L, et al. Transient and persistent dendritic spines in the neocortex in vivo. _Neuron_. 2005;45(2):279-91.

206. Egger V, Svoboda K, Mainen ZF. Dendrodendritic synaptic signals in olfactory bulb granule cells: local spine boost and global low-threshold spike. _Journal of Neuroscience_. 2005;25(14):3521.

207. Ohki K, Chung S, Ch'ng YH, Kara P, Reid RC. Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex. _Nature_. 2005;433(7026):597-603.

208. Ngo-Anh TJ, Bloodgood BL, Lin M, et al. SK channels and NMDA receptors form a Ca2+-mediated feedback loop in dendritic spines. _Nature neuroscience_. 2005;8(5):642-9.

209. Shepherd GMG, Svoboda K. Laminar and columnar organization of ascending excitatory projections to layer 2/3 pyramidal neurons in rat barrel cortex. _Journal of Neuroscience_. 2005;25(24):5670-9.

210. Gregor T, Bialek W, de Ruyter van Steveninck RR, Tank DW, Wieschaus EF. Diffusion and scaling during early embryonic pattern formation. _Proceedings of the National Academy of Sciences of the United States of America_. 2005;102(51):18403-7.

211. Shepherd GMG, Stepanyants A, Bureau I, Chklovskii D, Svoboda K. Geometric and functional organization of cortical circuits. _Nature neuroscience_. 2005;8(6):782-90.

212. Song S, Sjöström PJ, Reigl M, Nelson S, Chklovskii DB. Highly nonrandom features of synaptic connectivity in local cortical circuits. _PLoS biology_. 2005;3(3):e68.

213. Bureau I, Shepherd GMG, Svoboda K. Precise development of functional and anatomical columns in the neocortex. _Neuron_. 2004;42(5):789-801.

214. Nimchinsky EA, Yasuda R, Oertner TG, Svoboda K. The number of glutamate receptors opened by synaptic stimulation in single hippocampal spines. _Journal of Neuroscience_. 2004;24(8):2054.

215. Brünig I, Kaech S, Brinkhaus H, Oertner TG, Matus A. Influx of extracellular calcium regulates actin-dependent morphological plasticity in dendritic spines. _Neuropharmacology_. 2004;47(5):669--676.

216. Wang Y, Guo HF, Pologruto TA, et al. Stereotyped odor-evoked activity in the mushroom body of Drosophila revealed by green fluorescent protein-based Ca2\+ imaging. _Journal of Neuroscience_. 2004;24(29):6507.

217. Pologruto TA, Yasuda R, Svoboda K. Monitoring neural activity and \[Ca2+\] with genetically encoded Ca2\+ indicators. _Journal of Neuroscience_. 2004;24(43):9572.

218. Zito K, Knott G, Shepherd GMG, Shenolikar S, Svoboda K. Induction of spine growth and synapse formation by regulation of the spine actin cytoskeleton. _Neuron_. 2004;44(2):321-34.

219. Carter AG, Sabatini BL. State-dependent calcium signaling in dendritic spines of striatal medium spiny neurons. _Neuron_. 2004;44(3):483-93.

220. Shepherd GMG, Pologruto TA, Svoboda K. Circuit analysis of experience-dependent plasticity in the developing rat barrel cortex. _Neuron_. 2003;38(2):277-89.

221. Egger V, Svoboda K, Mainen ZF. Mechanisms of Lateral Inhibition in the Olfactory Bulb: Efficiency and Modulation of Spike-Evoked Calcium Influx into Granule Cells. _Journal of Neuroscience_. 2003;23(20):7551-7558.

222. Trachtenberg JT, Chen BE, Knott GW, et al. Long-term in vivo imaging of experience-dependent synaptic plasticity in adult cortex. _Nature_. 2002;420(6917):788-94.\\
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_Snapshot: 2012-06-06_
Current total primary research publications: *207*
!PubsByYear.jpg|height=400px!
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