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Context-dependent limb movement encoding in neuronal populations of motor cortex.

Omlor W, Wahl AS, Sipilä P, Lütcke H, Laurenczy B, Chen IW, Sumanovski LT, van 't Hoff M, Bethge P, Voigt FF, Schwab ME, Helmchen F.

Nat Commun. 2019 Oct 23;10(1):4812. doi: 10.1038/s41467-019-12670-z.


The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue.

Voigt FF, Kirschenbaum D, Platonova E, Pagès S, Campbell RAA, Kastli R, Schaettin M, Egolf L, van der Bourg A, Bethge P, Haenraets K, Frézel N, Topilko T, Perin P, Hillier D, Hildebrand S, Schueth A, Roebroeck A, Roska B, Stoeckli ET, Pizzala R, Renier N, Zeilhofer HU, Karayannis T, Ziegler U, Batti L, Holtmaat A, Lüscher C, Aguzzi A, Helmchen F.

Nat Methods. 2019 Nov;16(11):1105-1108. doi: 10.1038/s41592-019-0554-0. Epub 2019 Sep 16.


Functional Architecture and Encoding of Tactile Sensorimotor Behavior in Rat Posterior Parietal Cortex.

Mohan H, de Haan R, Broersen R, Pieneman AW, Helmchen F, Staiger JF, Mansvelder HD, de Kock CPJ.

J Neurosci. 2019 Sep 11;39(37):7332-7343. doi: 10.1523/JNEUROSCI.0693-19.2019. Epub 2019 Jul 22.


Layer-specific integration of locomotion and sensory information in mouse barrel cortex.

Ayaz A, Stäuble A, Hamada M, Wulf MA, Saleem AB, Helmchen F.

Nat Commun. 2019 Jun 13;10(1):2585. doi: 10.1038/s41467-019-10564-8.


High-density multi-fiber photometry for studying large-scale brain circuit dynamics.

Sych Y, Chernysheva M, Sumanovski LT, Helmchen F.

Nat Methods. 2019 Jun;16(6):553-560. doi: 10.1038/s41592-019-0400-4. Epub 2019 May 13.


Temporal refinement of sensory-evoked activity across layers in developing mouse barrel cortex.

van der Bourg A, Yang JW, Stüttgen MC, Reyes-Puerta V, Helmchen F, Luhmann HJ.

Eur J Neurosci. 2019 Sep;50(6):2955-2969. doi: 10.1111/ejn.14413. Epub 2019 May 2.


Tissue Clearing and Light Sheet Microscopy: Imaging the Unsectioned Adult Zebra Finch Brain at Cellular Resolution.

Rocha MD, Düring DN, Bethge P, Voigt FF, Hildebrand S, Helmchen F, Pfeifer A, Hahnloser RHR, Gahr M.

Front Neuroanat. 2019 Feb 14;13:13. doi: 10.3389/fnana.2019.00013. eCollection 2019.


iDISCO+ for the Study of Neuroimmune Architecture of the Rat Auditory Brainstem.

Perin P, Voigt FF, Bethge P, Helmchen F, Pizzala R.

Front Neuroanat. 2019 Feb 13;13:15. doi: 10.3389/fnana.2019.00015. eCollection 2019.


Ossified blood vessels in primary familial brain calcification elicit a neurotoxic astrocyte response.

Zarb Y, Weber-Stadlbauer U, Kirschenbaum D, Kindler DR, Richetto J, Keller D, Rademakers R, Dickson DW, Pasch A, Byzova T, Nahar K, Voigt FF, Helmchen F, Boss A, Aguzzi A, Klohs J, Keller A.

Brain. 2019 Apr 1;142(4):885-902. doi: 10.1093/brain/awz032.


A brain-wide functional map of the serotonergic responses to acute stress and fluoxetine.

Grandjean J, Corcoba A, Kahn MC, Upton AL, Deneris ES, Seifritz E, Helmchen F, Mann EO, Rudin M, Saab BJ.

Nat Commun. 2019 Jan 21;10(1):350. doi: 10.1038/s41467-018-08256-w.


Prion pathogenesis is unaltered in a mouse strain with a permeable blood-brain barrier.

Keller A, Nuvolone M, Abakumova I, Chincisan A, Reimann R, Avar M, Heinzer D, Hornemann S, Wagner J, Kirschenbaum D, Voigt FF, Zhu C, Regli L, Helmchen F, Aguzzi A.

PLoS Pathog. 2018 Nov 29;14(11):e1007424. doi: 10.1371/journal.ppat.1007424. eCollection 2018 Nov.


Behavioral Strategy Determines Frontal or Posterior Location of Short-Term Memory in Neocortex.

Gilad A, Gallero-Salas Y, Groos D, Helmchen F.

Neuron. 2018 Aug 22;99(4):814-828.e7. doi: 10.1016/j.neuron.2018.07.029. Epub 2018 Aug 9.


Sensory representation of an auditory cued tactile stimulus in the posterior parietal cortex of the mouse.

Mohan H, Gallero-Salas Y, Carta S, Sacramento J, Laurenczy B, Sumanovski LT, de Kock CPJ, Helmchen F, Sachidhanandam S.

Sci Rep. 2018 May 17;8(1):7739. doi: 10.1038/s41598-018-25891-x.


Fiber-optic implant for simultaneous fluorescence-based calcium recordings and BOLD fMRI in mice.

Schlegel F, Sych Y, Schroeter A, Stobart J, Weber B, Helmchen F, Rudin M.

Nat Protoc. 2018 May;13(5):840-855. doi: 10.1038/nprot.2018.003. Epub 2018 Mar 29.


Live imaging of neurogenesis in the adult mouse hippocampus.

Pilz GA, Bottes S, Betizeau M, Jörg DJ, Carta S, Simons BD, Helmchen F, Jessberger S.

Science. 2018 Feb 9;359(6376):658-662. doi: 10.1126/science.aao5056.


A Sensitive Dynamic and Active Pixel Vision Sensor for Color or Neural Imaging Applications.

Moeys DP, Corradi F, Li C, Bamford SA, Longinotti L, Voigt FF, Berry S, Taverni G, Helmchen F, Delbruck T.

IEEE Trans Biomed Circuits Syst. 2018 Feb;12(1):123-136. doi: 10.1109/TBCAS.2017.2759783.


Specific excitatory connectivity for feature integration in mouse primary visual cortex.

Muir DR, Molina-Luna P, Roth MM, Helmchen F, Kampa BM.

PLoS Comput Biol. 2017 Dec 14;13(12):e1005888. doi: 10.1371/journal.pcbi.1005888. eCollection 2017 Dec.


Optogenetically stimulating intact rat corticospinal tract post-stroke restores motor control through regionalized functional circuit formation.

Wahl AS, Büchler U, Brändli A, Brattoli B, Musall S, Kasper H, Ineichen BV, Helmchen F, Ommer B, Schwab ME.

Nat Commun. 2017 Oct 30;8(1):1187. doi: 10.1038/s41467-017-01090-6.


Neocortical dynamics during whisker-based sensory discrimination in head-restrained mice.

Helmchen F, Gilad A, Chen JL.

Neuroscience. 2018 Jan 1;368:57-69. doi: 10.1016/j.neuroscience.2017.09.003. Epub 2017 Sep 14. Review.


Multiphoton in vivo imaging with a femtosecond semiconductor disk laser.

Voigt FF, Emaury F, Bethge P, Waldburger D, Link SM, Carta S, van der Bourg A, Helmchen F, Keller U.

Biomed Opt Express. 2017 Jun 13;8(7):3213-3231. doi: 10.1364/BOE.8.003213. eCollection 2017 Jul 1.


An R-CaMP1.07 reporter mouse for cell-type-specific expression of a sensitive red fluorescent calcium indicator.

Bethge P, Carta S, Lorenzo DA, Egolf L, Goniotaki D, Madisen L, Voigt FF, Chen JL, Schneider B, Ohkura M, Nakai J, Zeng H, Aguzzi A, Helmchen F.

PLoS One. 2017 Jun 22;12(6):e0179460. doi: 10.1371/journal.pone.0179460. eCollection 2017.


Stimulus relevance modulates contrast adaptation in visual cortex.

Keller AJ, Houlton R, Kampa BM, Lesica NA, Mrsic-Flogel TD, Keller GB, Helmchen F.

Elife. 2017 Jan 28;6. pii: e21589. doi: 10.7554/eLife.21589.


Dendritic NMDA spikes are necessary for timing-dependent associative LTP in CA3 pyramidal cells.

Brandalise F, Carta S, Helmchen F, Lisman J, Gerber U.

Nat Commun. 2016 Nov 16;7:13480. doi: 10.1038/ncomms13480.


Layer-Specific Refinement of Sensory Coding in Developing Mouse Barrel Cortex.

van der Bourg A, Yang JW, Reyes-Puerta V, Laurenczy B, Wieckhorst M, Stüttgen MC, Luhmann HJ, Helmchen F.

Cereb Cortex. 2017 Oct 1;27(10):4835-4850. doi: 10.1093/cercor/bhw280.


Functional Imaging of Dentate Granule Cells in the Adult Mouse Hippocampus.

Pilz GA, Carta S, Stäuble A, Ayaz A, Jessberger S, Helmchen F.

J Neurosci. 2016 Jul 13;36(28):7407-14. doi: 10.1523/JNEUROSCI.3065-15.2016.


Long-range population dynamics of anatomically defined neocortical networks.

Chen JL, Voigt FF, Javadzadeh M, Krueppel R, Helmchen F.

Elife. 2016 May 24;5. pii: e14679. doi: 10.7554/eLife.14679.


Spatially segregated feedforward and feedback neurons support differential odor processing in the lateral entorhinal cortex.

Leitner FC, Melzer S, Lütcke H, Pinna R, Seeburg PH, Helmchen F, Monyer H.

Nat Neurosci. 2016 Jul;19(7):935-44. doi: 10.1038/nn.4303. Epub 2016 May 16.


Two-Photon Functional Imaging of Neuronal Activity.

Helmchen F.

In: Frostig RD, editor. In Vivo Optical Imaging of Brain Function. 2nd edition. Boca Raton (FL): CRC Press/Taylor & Francis; 2009. Chapter 2.


Specific Early and Late Oddball-Evoked Responses in Excitatory and Inhibitory Neurons of Mouse Auditory Cortex.

Chen IW, Helmchen F, Lütcke H.

J Neurosci. 2015 Sep 9;35(36):12560-73. doi: 10.1523/JNEUROSCI.2240-15.2015.


Model-based analysis of pattern motion processing in mouse primary visual cortex.

Muir DR, Roth MM, Helmchen F, Kampa BM.

Front Neural Circuits. 2015 Aug 5;9:38. doi: 10.3389/fncir.2015.00038. eCollection 2015.


Pathway-specific reorganization of projection neurons in somatosensory cortex during learning.

Chen JL, Margolis DJ, Stankov A, Sumanovski LT, Schneider BL, Helmchen F.

Nat Neurosci. 2015 Aug;18(8):1101-8. doi: 10.1038/nn.4046. Epub 2015 Jun 22.


Sparse, reliable, and long-term stable representation of periodic whisker deflections in the mouse barrel cortex.

Mayrhofer JM, Haiss F, Helmchen F, Weber B.

Neuroimage. 2015 Jul 15;115:52-63. doi: 10.1016/j.neuroimage.2015.04.045. Epub 2015 Apr 28.


Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance.

Madisen L, Garner AR, Shimaoka D, Chuong AS, Klapoetke NC, Li L, van der Bourg A, Niino Y, Egolf L, Monetti C, Gu H, Mills M, Cheng A, Tasic B, Nguyen TN, Sunkin SM, Benucci A, Nagy A, Miyawaki A, Helmchen F, Empson RM, Knöpfel T, Boyden ES, Reid RC, Carandini M, Zeng H.

Neuron. 2015 Mar 4;85(5):942-58. doi: 10.1016/j.neuron.2015.02.022.


A single-compartment model of calcium dynamics in nerve terminals and dendrites.

Helmchen F, Tank DW.

Cold Spring Harb Protoc. 2015 Feb 2;2015(2):155-67. doi: 10.1101/pdb.top085910.


Tactile frequency discrimination is enhanced by circumventing neocortical adaptation.

Musall S, von der Behrens W, Mayrhofer JM, Weber B, Helmchen F, Haiss F.

Nat Neurosci. 2014 Nov;17(11):1567-73. doi: 10.1038/nn.3821. Epub 2014 Sep 21.


Neuronal repair. Asynchronous therapy restores motor control by rewiring of the rat corticospinal tract after stroke.

Wahl AS, Omlor W, Rubio JC, Chen JL, Zheng H, Schröter A, Gullo M, Weinmann O, Kobayashi K, Helmchen F, Ommer B, Schwab ME.

Science. 2014 Jun 13;344(6189):1250-5. doi: 10.1126/science.1253050.


High-speed two-photon calcium imaging of neuronal population activity using acousto-optic deflectors.

Grewe BF, Helmchen F.

Cold Spring Harb Protoc. 2014 Jun 2;2014(6):618-29. doi: 10.1101/pdb.prot081778.


Microcircuit dynamics of map plasticity in barrel cortex.

Margolis DJ, Lütcke H, Helmchen F.

Curr Opin Neurobiol. 2014 Feb;24(1):76-81. doi: 10.1016/j.conb.2013.08.019. Epub 2013 Sep 22. Review.


Inference of neuronal network spike dynamics and topology from calcium imaging data.

Lütcke H, Gerhard F, Zenke F, Gerstner W, Helmchen F.

Front Neural Circuits. 2013 Dec 24;7:201. doi: 10.3389/fncir.2013.00201. eCollection 2013.


Activity in a premotor cortical nucleus of zebra finches is locally organized and exhibits auditory selectivity in neurons but not in glia.

Graber MH, Helmchen F, Hahnloser RH.

PLoS One. 2013 Dec 3;8(12):e81177. doi: 10.1371/journal.pone.0081177. eCollection 2013.


The challenge of connecting the dots in the B.R.A.I.N.

Devor A, Bandettini PA, Boas DA, Bower JM, Buxton RB, Cohen LB, Dale AM, Einevoll GT, Fox PT, Franceschini MA, Friston KJ, Fujimoto JG, Geyer MA, Greenberg JH, Halgren E, Hämäläinen MS, Helmchen F, Hyman BT, Jasanoff A, Jernigan TL, Judd LL, Kim SG, Kleinfeld D, Kopell NJ, Kutas M, Kwong KK, Larkum ME, Lo EH, Magistretti PJ, Mandeville JB, Masliah E, Mitra PP, Mobley WC, Moskowitz MA, Nimmerjahn A, Reynolds JH, Rosen BR, Salzberg BM, Schaffer CB, Silva GA, So PT, Spitzer NC, Tootell RB, Van Essen DC, Vanduffel W, Vinogradov SA, Wald LL, Wang LV, Weber B, Yodh AG.

Neuron. 2013 Oct 16;80(2):270-4. doi: 10.1016/j.neuron.2013.09.008.


Rapid 3D light-sheet microscopy with a tunable lens.

Fahrbach FO, Voigt FF, Schmid B, Helmchen F, Huisken J.

Opt Express. 2013 Sep 9;21(18):21010-26. doi: 10.1364/OE.21.021010.


Miniaturization of two-photon microscopy for imaging in freely moving animals.

Helmchen F, Denk W, Kerr JN.

Cold Spring Harb Protoc. 2013 Oct 1;2013(10):904-13. doi: 10.1101/pdb.top078147.


Online correction of licking-induced brain motion during two-photon imaging with a tunable lens.

Chen JL, Pfäffli OA, Voigt FF, Margolis DJ, Helmchen F.

J Physiol. 2013 Oct 1;591(19):4689-98. doi: 10.1113/jphysiol.2013.259804. Epub 2013 Aug 12.


Behaviour-dependent recruitment of long-range projection neurons in somatosensory cortex.

Chen JL, Carta S, Soldado-Magraner J, Schneider BL, Helmchen F.

Nature. 2013 Jul 18;499(7458):336-40. doi: 10.1038/nature12236. Epub 2013 Jun 23.


Steady or changing? Long-term monitoring of neuronal population activity.

Lütcke H, Margolis DJ, Helmchen F.

Trends Neurosci. 2013 Jul;36(7):375-84. doi: 10.1016/j.tins.2013.03.008. Epub 2013 Apr 19. Review.


HelioScan: a software framework for controlling in vivo microscopy setups with high hardware flexibility, functional diversity and extendibility.

Langer D, van 't Hoff M, Keller AJ, Nagaraja C, Pfäffli OA, Göldi M, Kasper H, Helmchen F.

J Neurosci Methods. 2013 Apr 30;215(1):38-52. doi: 10.1016/j.jneumeth.2013.02.006. Epub 2013 Feb 14.


Barrel cortex function.

Feldmeyer D, Brecht M, Helmchen F, Petersen CC, Poulet JF, Staiger JF, Luhmann HJ, Schwarz C.

Prog Neurobiol. 2013 Apr;103:3-27. doi: 10.1016/j.pneurobio.2012.11.002. Epub 2012 Nov 27. Review.


Reorganization of cortical population activity imaged throughout long-term sensory deprivation.

Margolis DJ, Lütcke H, Schulz K, Haiss F, Weber B, Kügler S, Hasan MT, Helmchen F.

Nat Neurosci. 2012 Nov;15(11):1539-46. doi: 10.1038/nn.3240. Epub 2012 Oct 21.


Two-photon imaging of spinal cord cellular networks.

Johannssen HC, Helmchen F.

Exp Neurol. 2013 Apr;242:18-26. doi: 10.1016/j.expneurol.2012.07.014. Epub 2012 Jul 28. Review.


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