Navigation auf


Brain Research Institute

Publications Group Helmchen


Groos D, Reuss AM, Rupprecht P, Stachniak T, Han S, Lewis CM, Sych Y, Wieckhorst M, Karayannis T, Aguzzi A, Helmchen F (2023) Distinct hypothalamus-habenula circuits govern risk preference. bioRxiv; doi: link

Schoenfeld G, Kollmorgen S, Lewis C, Bethge P, Reuss AM, Aguzzi A, Mante V, Helmchen F (2021) Dendritic integration of sensory and reward information facilitates learning. bioRxiv, link


Vladimirov N*, Voigt FF*,  Naert T,  Araujo GR, Cai R, Reuss AM,  Zhao S, Schmid P, Hildebrand S, Schaettin M, Groos D, Mateos JM,  Bethge P, Yamamoto T, Aerne V, Roebroeck A,  Ertürk A, Aguzzi A, Ziegler U, Stoeckli E, Baudis L, Lienkamp SS, Helmchen F (2024) Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for large cleared samples. Nature Communications, 15(1):2679. doi: 10.1038/s41467-024-46770-2  link (*equal contribution)

Gross D, Helmchen F (2024) The lateral habenula: A hub for value-guided behavior. Cell Reports, 15(1):2679. doi: 10.1038/s41467-024-46770-2 link (Review)

Rupprecht P, Duss SN, Becker D, Lewis CM, Bohacek J, Helmchen F (2024) Centripetal integration of past events in hippocampal astrocytes regulated by locus coeruleus. Nature Neuroscience, in press (preprint on   link

Masala N, Mittag M, Ambrad Giovannetti E, O'Neil DA, Distler FJ, Rupprecht P, Helmchen F, Yuste R, Fuhrmann M, Beck H, Wenzel M, Kelly T (2024) Aberrant hippocampal Ca2+ micro-waves following synapsin-dependent adeno-associated viral expression of Ca2+ indicators. eLife, Reviewed Preprint, doi: link

Han S, Helmchen F (2023) Behavior-relevant top-down cross-modal predictions in mouse neocortex. Nature Neuroscience 27:298–308, doi: link


Wilhelm M*, Sych Y*, Fomins A, Alatorre Warren JL,  Lewis CM, Serratosa Capdevila L, Boehringer R, Amadei EA, Grewe BF, O'Connor EC, Hall B, Helmchen F (2023) Striatum-projecting prefrontal cortex neurons support working memory maintenance. Nature Communications, 14, 7016.  link (* equal contribution)

Marmor O, Pollack Y, Doron C, Helmchen F, Gilad A (2023) History information emerges in the cortex during learning. eLife, 12:e83702. link 

Lewis CM, Hoffmann A, Helmchen F (2023) Linking brain activity across scales with simultaneous opto- and electrophysiology. Neurophotonics, 11(3):033403. (Review) link

Ibanez V, Bohlen L, Manuella F, Mansuy IM, Helmchen F, Wahl AS (2023) EXPLORE: A novel deep learning-based analysis method for exploration behaviour in object recognition tests. Scientific Reports, 13(1):4249. link

Voigt F, Reuss AM, Naert T, Hildebrand S, Schaettin M, Hotz AL, Whitehead L, Bahl A, Neuhauss SCF, Roebroeck A, Stoeckli ET, Lienkamp SS, Aguzzi A, Helmchen F (2024) Reflective multi-immersion microscope objectives inspired by the Schmidt telescope. Nature Biotechnology, 42(1):65-71. link  
Schmidt objective


Wu Y, Bottes S, Fisch R, Zehnder C, Cole JD, Pilz GA, Helmchen F, Simons BD, Jessberger S (2023) Chronic in vivo imaging defines age-dependent alterations of neurogenesis in the mouse hippocampus. Nature Aging, 3(4)  
Nature Aging Volume 3 Issue 4


Banerjee A, Wang BA, Teutsch J, Helmchen F, Pleger B (2023) Analogous cognitive strategies for tactile learning in the rodent and human brain. Progress in Neurobiology, 102401. doi: 10.1016/j.pneurobio.2023.102401. (Review) link


Kirschenbaum D*, Dadgar-Kiani E*, Catto F*, Voigt F*, Trevisan C, Bichsel O, Shirani H, Nilsson KPR, Frontzek KJ, Paganetti P, Helmchen F, Lee J-H§, Aguzzi A§ (2022) Whole-brain microscopy reveals distinct temporal and spatial efficacy of anti-Aβ therapies. EMBO Molecular Medicine, 15(1):e16789.  doi: 10.15252/ (* equal contribution) (§ co-senior authors)

Cai R*, Kolabas ZI*, Pan C, Mai H, Zhao S, Kaltenecker D, Voigt FF, Molbay M, Ohn T, Vincke C, Todorov MI, Helmchen F, Van Ginderachter JA, Ertürk A (2022) Whole mouse clearing and imaging at cellular level with vDISCO, Nature Protocols, Online ahead of print, doi: 10.1038/s41596-022-00788-2link (*equal contribution)

Sych Y, Fomins A, Novelli L, Helmchen F (2022) Mesoscale brain dynamics reorganizes and stabilizes during learning, Cell Reports, 40(12):111394. link

Fomins A, §Sych Y, §Helmchen F (2022) Conservative significance testing of tripartite interactions in multivariate neural data. Network Neuroscience, 6(4): 1243–1274link (§ co-senior authors)

Ni R, Dean-Ben XL, Kirschenbaum D, Rudin M, Chen Z, Crimi A, Voigt FF, Nilsson KPR, Helmchen F,  Nitsch R, Aguzzi A, Razansky D, Klohs J (2022) Whole brain optoacoustic tomography reveals strain-specific regional beta-amyloid densities in Alzheimer’s disease amyloidosis models, Nature Biomedical Engineering, 6(9) 

Dean KM, Chakraborty T, Daetwyler S, Lin J, Garrelts G, M'Saad O, Mekbib HT, Voigt FF, Schaettin M, Stoeckli ET, Helmchen F, Bewersdorf J, Fiolka R (2022). Isotropic imaging across spatial scales with axially swept light-sheet microscopy. Nature Protocols, 17:2025–

Lalive AL, Congiu M, Lewis C, Groos D, Clerke JA, Tchenio A, Ge Y, Helmchen F, Mameli M (2022) Synaptic inhibition in the lateral habenula shapes reward anticipation. Current Biology 32(8):1829-1836.e4. link


Fagerholm ED, Foulkes WMC, Gallero-Salas Y, Helmchen F, Moran RJ, Friston KJ, Leech R. (2022) Estimating anisotropy directly via neural timeseries.  Journal of Computational Neuroscience, 50:241–249. link


Naert T, Çiçek Ö, Ogar P, Bürgi M, Shaidani  N-I, Kaminski  MM, Xu Y, Grand K, Vujanovic  M, Prata A, Hildebrandt F, Brox T, Ronneberger O, Voigt FF, Helmchen F, Loffing J, Horb ME, Rankin Willsey H, Lienkamp SS (2021) Deep learning is widely applicable to phenotyping embryonic development and disease. Development, 148(21):dev199664. link

Brandalise F, Carta S, Leone R, Helmchen F, Holtmaat A, Gerber U (2021). Dendritic branch-constrained NMDA spikes drive synaptic plasticity in hippocampal CA3 pyramidal cells. Neuroscience, 489:57-68.  link

Schoenfeld G*, Carta S*, Rupprecht O, Ayaz A, Helmchen F (2021). In vivo calcium imaging of CA3 pyramidal neuron populations in adult mouse hippocampus. eNeuro, 8(4):ENEURO.0023-21.2021. link (* equal contribution)


Perin P, Rossetti R, Ricci C, Cossellu D, Lazzarini S, Bethge P, Voigt FF, Helmchen F, Batti L, Gantar I, Pizzala R. (2021) 3D Reconstruction of the clarified rat hindbrain choroid plexus. Frontiers Cell Dev Biol. 9:692617. link

Zerbi V, Pagani M, Markicevic M, Matteoli M, Pozzi D, Fagiolini M, Bozzi Y, Galbusera A, Scattoni ML, Provenzano G, Banerjee A, Helmchen F, Albert Basson M, Ellegood J, Lerch JP, Rudin M, Gozzi A§, Wenderoth N§ (2021) Brain mapping across 16 autism mouse models reveals a spectrum of functional connectivity subtypes, Molecular Psychiatry, 26:7610-7620. link (§ co-senior authors)

Rupprecht P, Carta S, Hoffmann A, Echizen M, Kitamura K, Helmchen F§, Friedrich RW§ (2021) A deep learning toolbox for noise-optimized, generalized spike inference from calcium imaging data, Nature Neuroscience, 24(9):1324-1337. link (§ co-senior authors)

Brattoli B*, Buechler U*, Dorkenwald M, Reiser P, Filli L, Helmchen F, Wahl AS§, Ommer B§ (2020). uBAM: Unsupervised Behavior Analysis and Magnification using Deep Learning, Nature Machine Intelligence, 3:495–506. link (* equal contribution) (§ co-senior authors)

Fagerholm ED, Foulkes WMC, Gallero-Salas Y, Helmchen F, Friston KJ, Leech R, Moran RJ (2020) Network constraints in scale free dynamical systems, Frontiers in Computational Neuroscience, 15:643148. link 

Gallero-Salas Y, Han S, Sych Y, Voigt FF, Laurenczy B, Gilad A§, Helmchen F§ (2021) Sensory and behavioral components of neocortical signal flow in discrimination tasks with short-term memory, Neuron, 109(1):135-148.e6. link (§ co-senior authors)

Bottes S*, Jaeger BN*, Pilz GA*, Jörg DJ, Cole JD, Kruse M, Harris L, Korobeynyk VI, Mallona I, Helmchen F, Guillemot F, Simons BD, Jessberger S (2021) Long-term self-renewing stem cells in the adult mouse hippocampus identified by intravital imaging, Nature Neuroscience, 24(2):225-233. link (* equal contribution) 


Ineichen C, Greter A, Baer M, Sigrist H, Sautter E, Sych, Y, Helmchen F, Pryce CR (2020). Basomedial amygdala activity in mice reflects specific and general aversion uncontrollability. European Journal of Neuroscience, 2022; 55:2435–2454. link

Kastli R*, Vighagen R*, van der Bourg A*, Argunsah AO*, Iqbal A, Voigt FF, Kirschenbaum D, Aguzzi A, Helmchen F, Karayannis T (2020) Developmental divergence of sensory stimulus representation in cortical interneurons, Nature Communications, 11:5729.  link (* equal contribution) 

Banerjee A, Parente G, Teutsch J, Lewis C, Voigt FF, Helmchen F (2020) Value-guided remapping of sensory circuits by lateral orbitofrontal cortex, Nature, 585:245  link

Frezel N, Platonova E, Voigt FF, Mateos JM, Kastli R, Ziegler U, Karayannis T, Helmchen F, Wildner H, Zeilhofer HU (2020) In-depth characterization of layer 5 output neurons of the primary somatosensory cortex innervating the mouse dorsal spinal cord, Cerebral Cortex Communications1(1):tgaa052. link 

Renz AF, Lee J, Tybrandt K, Brzezinski M, Lorenzo Mercado DA, Cheraka MC, Lee J, Helmchen F, Vörös J,  Lewis CM (2020) Opto-E-Dura: a soft, stretchable ECoG array for multimodal, multi-scale neuroscience, Advanced Health Materials, 9(17):e2000814. link 

Fagerholm ED, Foulkes WMC, Gallero-Salas Y, Helmchen F, Friston KJ, Moran RJ, Leech R (2020) Conservation laws by virtue of scale symmetries in neural systems, PLOS Computational Biology, 16(5):e1007865 link 

Gilad A, Helmchen F (2020) Spatiotemporal refinement of signal flow through association cortex during learning, Nature Communications, 11:1744, link

Markicevic M, Fulcher BD, Lewis C, Helmchen F, Rudin M, Zerbi V, Wenderoth N (2020) Cortical excitation:inhibition imbalance causes network-specific functional hypoconnectivity: a DREADD-fMRI study. Cerebral Cortex30(9):4922-4937. link


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 (2019) Context-dependent limb movement encoding in neuronal populations of motor cortex. 10(1):4812. link 

Voigt FF, Kirschenbaum D, Platonova E, Pagès S, Campbell RAA, Kästli R, Schaettin R, 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 E, Pizzala R, Renier N, Zeilhofer HU, Karayannis T, Ziegler U, Batti L, Holtmaat A, Lüscher C, Aguzzi A, Helmchen F (2019) The mesoSPIM initiative: open-source light-sheet microscopes for imaging cleared tissue. Nature Methods, 16(11):1105-1108. doi: 10.1038/s41592-019-0554-0

Mohan H, de Haan R, Broersen R, Pieneman AW, Helmchen F, Staiger JF, Mansvelder HD, de Kock CPJ (2019) Functional architecture and encoding of tactile sensorimotor behavior in rat posterior parietal cortex. Journal of Neuroscience 39:7332-7343. link

Ayaz A, Staeuble A, Saleem AB, Helmchen F (2019) Layer-specific integration of locomotion and concurrent wall touching in mouse barrel cortex. 10:2585

Sych Y, Chernysheva M, Sumanovski LT, Helmchen F (2019) High-density multi-fiber photometry for studying large-scale brain circuit dynamics. Nature Methods,16(6):553-560. 

van der Bourg A*, Yang J-W*, Stüttgen MC, Reyes-Puerta V, Helmchen F§, Luhmann HJ§ (2019) Temporal refinement of sensory-evoked activity across layers in developing mouse barrel cortex. European Journal of Neuroscience, doi: 10.1111/ejn.14413 link   (* co-first authors, § co-senior authors)

Perin P, Voigt FF, Bethge P, Helmchen F, Pizzala R (2019) iDISCO+ for the study of neuroimmune architecture of the rat auditory brainstem, Frontiers in Neuroanatomy, 13, link      

Rocha MD, Düring DN, Bethge P, Voigt FF, Hildebrand S, Helmchen F, Pfeifer A, Hahnloser R, Gahr M (2019)Tissue clearing and light sheet microscopy: Imaging the unsectioned adult zebra finch brain at cellular resolution. Frontiers in Neuroanatomy, 13, link    

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. (2019). Ossified blood vessels in primary familial brain calcification elicit a neurotoxic astrocyte response. Brain, 142(4):885-902. link

Grandjean J, Corcoba A, Kahn MC, Upton AL, Deneris ES, Seifritz E, Helmchen F, Mann EO, Rudin M, Saab BJ (2019) A brain-wide functional map of the serotonergic responses to acute stress and fluoxetine.Nature Communications, 10(1):350. link


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 (2018). Prion pathogenesis is unaltered in a mouse strain with a permeable blood-brain barrier. PLoS Pathogens, 14(11):e1007424. link

Gilad A, Gallero-Salas Y, Groos D, Helmchen F (2018). Behavioral Strategy Determines Frontal or Posterior Location of Short-Term Memory in Neocortex. Neuron, 99(4):814-828. link

Mohan H, Gallero-Salas Y, Carta S, Sacramento J, Laurenczy B, Sumanovski L, de Kock C, Helmchen F, Sachidhanandam S (2018). Sensory representation of an auditory cued tactile stimulus in the posterior parietal cortex of the mouse. Scientific Reports, 8:7739. link

Pilz GA*, Bottes S*, Betizeau M, Jörg DJ, Carta S, Simons BD, Helmchen F, Jessberger S (2018) Live imaging of neurogenesis in the adult hippocampus. Science 359:658-662. link   (*equal contribution)

Schlegel F, Sych Y, Schroeter A, Stobart J, Weber B, Helmchen F, Rudin M (2018) Fiber-optic implant for simultaneous fluorescence-based calcium recordings and BOLD fMRI in mice. Nature Protocols 13(5):840-855. link

Moeys DP, Corradi F, Li C, Bamford SA, Longinotti L, Voigt FF, Berry S, Taverni G, Helmchen F, Delbruck T. (2018) A Sensitive Dynamic and Active Pixel Vision Sensor for Color or Neural Imaging Applications.IEEE Transactions on Biomedical Circuits and Systems 12(1):123-136. doi: 10.1109/TBCAS.2017.2759783. link


Muir DR, Molina-Luna P, Roth MM, Helmchen F, Kampa BM (2017) Specific excitatory connectivity for feature integration in mouse primary visual cortex. PLOS Computational Biology, 2017 Dec 14;13(12):e1005888. link

Wahl AS, Büchler U, Brändli A, Brattoli B, Musall S, Kasper H, Ineichen BV, Helmchen F, Ommer B,  Schwab ME (2017) Optogenetically stimulating intact rat corticospinal tract post-stroke restores motor control through regionalized functional circuit formation. Nature Communications, 8(1):1187 link

Helmchen F, Gilad A, Chen JL (2017) Neocortical Dynamics during Whisker-based Sensory Discrimination in Head-Restrained Mice. Neuroscience, S0306-4522(17)30637-1 (Review) link

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 (2017) An R-CaMP1.07 reporter mouse for cell-type-specific expression of a sensitive red fluorescent calcium indicator. PLOS ONE 12(6): e0179460. (* equal contribution) link

Voigt FF*, Emaury F*, Bethge P, Waldburger D, Link SM, Carta S, van der Bourg A, Helmchen F, Keller U (2017) Multiphoton in vivo imaging with a femtosecond semiconductor disk laser. Biomed. Opt. Express 8, 3213-3231. (* equal contribution) link 

Keller AJ, Houlton R, Kampa BM, Lesica NA, Mrsic-Flogel TD, Keller GB, Helmchen F (2017) Stimulus relevance modulates contrast adaptation in visual cortex. Elife, pii: e21589. link


Brandalise F, Carta S, Helmchen F, Lisman J, Gerber U (2016) Dendritic NMDA spikes are necessary for timing-dependent associative LTP in CA3 pyramidal cells. Nature Communications 7, 13480, doi: 10.1038/ncomms13480. link

van der Bourg A*, Yang J-W*, Reyes-Puerta V, Laurenczy B, Wieckhorst M, Stüttgen MC, Luhmann HJ, Helmchen F (2016). Layer-specific refinement of sensory coding in developing mouse barrel cortex. Cerebral Cortex, Advanced Online.  (* equal contribution)

Pilz GA*, Carta S*, Stäuble A, Ayaz A, Jessberger S**, Helmchen F** (2016) Functional imaging of dentate granule cells in the adult mouse hippocampus. Journal of Neuroscience, 36(28), 7407-7414.  (* equal contribution) (** Co-senior author)  link

Chen JL*, Voigt FF*, Javadzadeh M, Krueppel R, Helmchen F (2016) Long-range population dynamics of anatomically defined neocortical networks. Elife, pii: e14679. (* equal contribution)  link

Leitner FC, Melzer S, Lütcke H, Pinna R, Seeburg PH, Helmchen F, Monyer H (2016) Spatially segregated feedforward and feedback neurons support differential odor processing in the lateral entorhinal cortex. Nature Neuroscience, 19(7), 935-944.  link


Chen I, Helmchen F, Lütcke H (2015) Specific early and late oddball-evoked responses in excitatory and inhibitory neurons of mouse auditory cortex. Journal of Neuroscience, 35(36):12560-12573. link

Muir DR, Roth M, Helmchen F, Kampa B (2015) Model-based analysis of pattern motion processing in mouse primary visual cortex, Frontiers in Neural Circuits, 9:38. doi: 10.3389/fncir.2015.00038, link

Chen JL, Margolis DJ, Stankov A, Sumanovski LT, Schneider BL, Helmchen F (2015) Pathway-specific reorganization of projection neurons in somatosensory cortex during learning. Nature Neuroscience, 18(8):1101-1108. link


Helmchen F, Chen JL (2015) Imaging the cortical representation of active sensing in the vibrissa system. In: Sensorimotor Integration in the Whisker System (eds. Krieger P, Groh A), Springer. (Book chapter)

Voigt FF, Chen JL, Krueppel R, Helmchen F (2015) A modular two-photon microscope for simultaneous imaging of distant cortical areas in vivo. SPIE Conference, MULTIPHOTON MICROSCOPY IN THE BIOMEDICAL SCIENCES XV Book Series: Proceedings of SPIE, Volume: 9329, Article Number: 93292C

Mayrhofer JM, Haiss F, Helmchen F, Weber B (2015) Sparse, reliable, and long-term stable representation of periodic whisker deflections in the mouse barrel cortex. Neuroimage, 115:52-63, doi: 10.1016/j.neuroimage.2015.04.045

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 (2015) Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance. Neuron, 85(5):942-58, link


Musall S, von der Behrens W, Mayrhofer JM, Weber B, Helmchen F, Haiss F (2014) Tactile frequency discrimination is enhanced by circumventing neocortical adaptation. Nature Neuroscience, 17(11):1567-73, link

Wahl AS, Omlor W, Rubio JC, Chen JL, Zheng H, Schröter A, Gullo M, Weinmann O, Kobayashi K, Helmchen F, Ommer B, Schwab ME (2014) Asynchronous therapy restores motor control by rewiring of the rat corticospinal tract after stroke. Science, 344(6189):1250-5, link

Margolis DJ, Lütcke H, Helmchen F (2014) Microcircuit dynamics of map plasticity in barrel cortex. Current Opinion in Neurobiology, 24: 76-81, link (Review)


New Book Release:

Optical Imaging of Neocortical Dynamics. Bruno Weber and Fritjof Helmchen eds., Neuromethods, vol. 85, Springer Science+Business Media New York (2014) link

  • Helmchen F, Weber B. Neocortex in the Spotlight: Concepts, Questions, and Methods. (Chapter 1)
  • Grewe BF, Helmchen F, Kampa BM. Two-Photon Imaging of Neuronal Network Dynamics in Neocortex. (Chapter 9)
  • Margolis DJ, Lütcke H, Helmchen F, Weber B, Haiss F. Chronic Two-Photon Imaging of Neural Activity in the Anesthetized and Awake Behaving Rodent. (Chapter 10)
Optical Imaging of Neocortical Dynamics


Lütcke H, Gerhard F, Zenke F, Gerstner W, Helmchen F (2013) Inference of neuronal network spike dynamics and topology from calcium imaging data. Frontiers in Neural Circuits, 7:201. doi: 10.3389/fncir.2013.00201, link

Chen JL, Andermann ML,Keck T,Xu N, Ziv Y (2013) Imaging neuronal populations in behaving rodents: Paradigms for studying neural circuits underlying behavior in the mammalian cortex. Journal of Neuroscience, 33(45):17631–17640, link (Mini-Symposium)

Devor A et al. (2013) The challenge of connecting the dots in the B.R.A.I.N. Neuron, 80: 270-274link (Viewpoint)

Graber M, Helmchen F, Hahnloser RH (2013) Activity in a premotor cortical nucleus of zebra finches is locally organized and exhibits auditory selectivity in neurons but not in glia. PLoS ONE, 8(12): e81177, link

Oertner TG, Helmchen F, de Lecea L, Beck H, Konnerth A, Kaupp B, Knöpfel T, Yawo H, Häusser M (2013) Optogenetic analysis of mammalian neural circuits. In: Optogenetics (Dahlem Workshop Reports) (ed. Hegemann P), De Gruyter. (Book chapter)

Chen JL*, Pfäffli OA*, Voigt FF, Margolis DJ, Helmchen F (2013) Online correction of licking-induced brain motion during two-photon imaging with a tunable lens. Journal of Physiology, 591(Pt 19):4689-98. link (* equal contribution)

Fahrbach FO, Voigt FF, Schmid B, Helmchen F, Huisken J (2013) Rapid 3D light-sheet microscopy with a tunable lens. Optics Express, 21(18): 21010-21026link

Chen JL, Carta S, Soldado-Magraner J, Schneider BL, Helmchen F (2013) Behavior-dependent recruitment of long-range projection neurons in somatosensory cortex. Nature, 499:336-340link

Helmchen F, Hübener M (2013) Neuronal networks in the spotlight: Deciphering cellular activity patterns with fluorescent proteins. e-Neuroforum, 4:31–38, (Review)
(also published in german: Neuronal Netzwerke im Rampenlicht: Mit leuchtenden Proteinen zelluläre Aktivitätsmuster entschlüsseln. Neuroforum, 02/2013, 47-55)

Lütcke H, Margolis DJ, Helmchen F (2013) Steady or changing? Long-term monitoring of neuronal population activity. Trends in Neurosciences, 36(7):375-384, (Review) link

Langer D, van’t Hoff M, Keller AJ, Nagarajad C, Pfäffli OA, Göldi M, Kasper H, Helmchen F (2013) HelioScan: a software framework for controlling in vivo microscopy setups with high hardware flexibility, functional diversity and extendibility. Journal of Neuroscience Methods, 215(1):38-52pdf (PDF, 2 MB)

Feldmeyer D, Brecht M, Helmchen F, Petersen C, Poulet J, Staiger JF, Luhmann H, Schwarz C (2013) Barrel cortex function. Progress in Neurobiology, 103:3-27, doi:pii: S0301-0082(12)00170-0 , Epub 2012 Nov 27, (Review) pdf (PDF, 2 MB)


Margolis DJ*, Lütcke H*, Schulz K, Haiss F, Weber B, Kügler S, Hasan MT, Helmchen F (2012) Reorganization of cortical population activity imaged throughout long-term sensory deprivation. Nature Neuroscience, 15(11):1539-1546. doi:10.1038/nn.3240 pdf (PDF, 2 MB) (* equal contribution)

Helmchen F (2012) Calcium Imaging. In: Handbook of Neural Activity Measurement (eds. Brette R, Destexhe A), Cambridge University Press.(Book chapter)

Johannssen HC, Helmchen F (2012) Two-photon imaging of spinal cord cellular networks. Experimental Neurology, 242:18-26, (Review)pdf

Roth MM, Helmchen F, Kampa BM (2012) Distinct functional properties of primary and posteromedial visual area of mouse neocortex. Journal of Neuroscience, 32(28):9716-9726pdf (PDF, 1 MB)

Schulz K, Sydekum E, Krueppel R, Engelbrecht CJ, Schlegel F, Schröter A, Rudin M, Helmchen F (2012) Simultaneous BOLD fMRI and fiber-optic calcium recording in rat neocortex. Nature Methods, 9:597–602pdf (PDF, 1 MB)

Coiret G, Ster J, Grewe B, Wendling F, Helmchen F, Gerber U, Benquet P (2012) Neuron to astrocyte communication via cannabinoid receptors is necessary for sustained epileptiform activity in rat hippocampus. PloS ONE, 7(5):e37320pdf (PDF, 508 KB)

Farinelli M, Heitz FD, Grewe BF, Tyagarajan SK, Helmchen F, Mansuy IM (2012) Selective regulation of NR2B by protein phosphatase-1 for the control of the NMDA receptor in neuroprotection. PloS ONE, 7 (3):e34047pdf

Minderer M*, Liu W*, Sumanovski LT, Kügler S, Helmchen F, Margolis DJ (2012) Chronic imaging of cortical sensory map dynamics using a genetically encoded calcium indicator. Journal of Physiology, 590:99-107. pdf (PDF, 2 MB) (* equal contribution)

Langer D, Helmchen F (2012) Post hoc immunostaining of GABAergic neuronal subtypes following in vivo two-photon calcium imaging in mouse neocortex. Pflügers Archiv, 463(2):339-54. Epub 2011 Dec 2. pdf (PDF, 1 MB)


Kampa B, Roth M, Göbel W, Helmchen F (2011) Representation of visual scenes by local neuronal populations in layer 2/3 of mouse visual cortex. Frontiers in Neural Circuits, 5:18. doi: 10.3389/fncir.2011.00018. pdf (PDF, 2 MB)

Grewe BF*, Voigt FF*, van 't Hoff M, Helmchen F (2011) Fast two-layer two-photon imaging of neuronal cell populations using an electrically tunable lens. Biomedical Optics Express, 2(7): 2035-2046. pdf (PDF, 1 MB) (* equal contribution)

Lütcke H, Helmchen F (2011) Two-photon imaging and analysis of neural network dynamics. Reports on Progress in Physics, 74(8):086602 (19pp) doi:10.1088/0034-4885/74/8/086602 (Review) pdf (PDF, 1 MB)

Ster J, Mateos JM, Grewe BF, Coiret G, Corti C, Corsi M, Helmchen F, Gerber U (2011) Enhancement of CA3 hippocampal network activity by activation of group II metabotropic glutamate receptors. Proc. Natl. Acad. Sci. USA, 108(24): 9993-97. pdf (PDF, 1 MB)


Book Release:

Imaging in Neuroscience: A Laboratory Manual. Helmchen F, Konnerth A eds. Cold Spring Harbor Laboratory Press, Cold Spring Harbor. 92 Chapters, 1084 pp. (2011)

  • Helmchen F, Tank DW. A Single-Compartment Model of Calcium Dynamics in Nerve Terminals and Dendrites. (Chapter 36)
  • Kampa BM, Göbel W, Helmchen F. Three-Dimensional Imaging of Neuronal Network Activity. (Chapter 52)
  • Grewe BF, Helmchen F. High-Speed Two-Photon Calcium Imaging of Neuronal Population Activity Using Acousto-Optic Deflectors. (Chapter 53)
  • Nimmerjahn A, Helmchen F. In Vivo Labeling of Cortical Astrocytes with Sulforhodamine 101. (Chapter 63)
  • Helmchen F, Denk W, Kerr JND. Miniaturization of Two-Photon Microscopy for Imaging in Freely Moving Animals. (Chapter 78)
Imaging in Neuroscience


Ruchty M, Helmchen F, Wehner R, Kleineidam CJ (2010) Representation of thermal information in the antennal lobe of leaf-cutting ants. Frontiers in Behavioral Neuroscience, 4:174pdf

Johannssen HC, Helmchen F (2010) In vivo Ca2+ imaging of dorsal horn neuronal populations in mouse spinal cord. Journal of Physiology, 588: 3397-3402.pdf (PDF, 3 MB)

Engelbrecht CJ*, Voigt FF*, Helmchen F (2010) Miniaturized selective plane illumination microscopy for high-contrast in vivo fluorescence imaging. Optics Letters, 35(9): 1413-1415.pdf (PDF, 312 KB) (* equal contribution)

Lee CM, Engelbrecht CJ, Soper TD, Helmchen F, Seibel EJ (2010) Scanning fiber endoscopy with highly flexible, 1 mm catheterscopes for wide-field, full-color imaging. J. Biophotonics, 3(5-6): 358-407.pdf (PDF, 2 MB)

Grewe B, Langer D, Kasper H, Kampa B, Helmchen F (2010) High-speed in vivo calcium imaging reveals neuronal network activity with near-milisecond precision. Nature Methods, 7(5): 399-405. pdf (PDF, 2 MB)

Lütcke H*, Murayama M*, Hahn T, Margolis DJ, Astori S, Meyer zum Alten Borgloh, S, Göbel W, Yang Y, Tang W, Kügler S, Sprengel R, Nagai T, Miyawaki A, Larkum ME, Helmchen F, Hasan MT (2010) Optical recording of neuronal activity with a genetically-encoded calcium indicator in anesthetized and freely moving mice. Frontiers in Neural Circuits, 4(9): 1-12. pdf (PDF, 5 MB) (* equal contribution)


Grewe B, Helmchen F (2009) Optical probing of neuronal ensemble activity. Curr. Opin. Neurobiol., 19(5): 520-529. (Review) pdf (PDF, 714 KB)

Engelbrecht CE, Göbel W, Helmchen F (2009) Enhanced fluorescence signal in nonlinear microscopy through supplementary fiber-optic light collection. Optics Express, 17(8): 6421-6435. pdf (PDF, 1 MB)

Hoogland, TM, Kuhn, B, Göbel, W, Huang, W, Nakai, J, Helmchen, F, Flint, SJ, Wang SSH (2009) Radially expanding transglial calcium waves in the intact cerebellum. Proc. Natl. Acad. Sci. USA 106(9): 3496-3501. pdf (PDF, 2 MB)

Göbel W, Kampa B, Helmchen F (2009) In vivo imaging of cellular network signalling. In: Handbook of Cell Signaling., 2nd edition (eds. Bradshaw RA, Dennis EA), Elsevier.

Helmchen F, Wang SSH, Denk W (2009) Multiphoton Microscopy in Neuroscience. In: Biomedical Optical Imaging (eds. Fujimoto JG, Farkas D), Oxford University Press.

Helmchen F (2009) Two-photon functional imaging of neuronal activity. In: In Vivo Optical Imaging of Brain Function, 2nd edition (ed. Ron Frostig) Elsevier, CRC Press.


Helmchen F, Petersen CCH (2008) New views into the brain of mice on the move. Nature Methods, 5(11):925-926. (Comment) pdf (PDF, 849 KB)

Helmchen F, Kleinfeld, D (2008) In vivo measurements of blood flow and glial cell function with two-photon laser scanning microscopy. Methods in Enzymology, 444:231-254

Göbel W, Helmchen F (2008) Optische Messung neuronaler Netzwerkdynamik in 3D. Neuroforum, 02/2008184-189

Engelbrecht CE, Johnston RS, Seibel EJ, Helmchen F (2008) Ultra-compact fiber-optic two-photon microscope for functional fluorescence imaging in vivo. Optics Express, 16:5556-5564. pdf (PDF, 478 KB)

Nimmerjahn A, Theer P, Helmchen F (2008) Two-photon laser scanning microscopy. In: Ultrafast Laser Pulses in Biology and Medicine (eds. Braun M, Gilch P, Zinth W), Springer Verlag.

Waters J, Nevian T, Sakmann B, Helmchen F (2008) Action potentials in dendrites and spike-timing dependent plasticity. In: Learning and Memory, 4 Vols: A Comprehensive Reference (eds. ), Elsevier. 2008

Margolis DJ (2008) Increased bursting in layer 2/3 neurones of awake neocortex. Journal of Physiology, 586(Pt 18):4341-4342. pdf (PDF, 59 KB)


Göbel W, Helmchen F (2007) In vivo calcium imaging of neural network function. Physiology, 22:358-365. (Review) pdf (PDF, 2 MB)

Kerr JND, de Kock, CPJ, Greenberg, DS, Bruno, RM, Sakmann B, Helmchen F (2007) Spatial organization of neuronal population responses in layer 2/3 of rat barrel cortex. Journal of Neuroscience, 27(48):13316-13328. pdf (PDF, 6 MB)

Helmchen F (2007) Biochemical compartmentalization in dendrites. In: Dendrites (eds. Stuart G, Spruston N, Häusser M), 2nd edition, Oxford University Press.

Göbel W, Helmchen F (2007) New angles on neuronal dendrites in vivo. Journal of Neurophysiology 98:3770-3779. pdf (PDF, 3 MB)

Göbel W, Kampa BM, Helmchen (2007) Neuronale Netzwerkdynamik in 3D. In: BIOForum 05/2007, pp. 18-19.


Larkum ME, Waters J, Sakmann B, Helmchen F (2007) Dendritic spikes in apical dendrites of neocortical layer 2/3 pyramidal neurons. Journal of Neuroscience 27(34):8999-9008. pdf (PDF, 531 KB)

Nevian T, Helmchen F (2007) Calcium indicator loading of neurons using single-cell electroporation. Pflügers Archiv 454(4): 675-688. pdf (PDF, 652 KB)

Helmchen F, Nevian T (2007) Little strokes fill big oaks: a simple in vivo stain of brain cells. Neuron 53(6): 771-773. (Comment) pdf (PDF, 156 KB)

Göbel W, Kampa BM, Helmchen F (2007) Imaging cellular network dynamics in three dimensions using fast 3D laser scanning. Nature Methods 4: 73-79. pdf (PDF, 894 KB)



Waters J, Helmchen F (2006) Background synaptic activity is sparse in neocortex. Journal of Neuroscience 26(32): 8267-8277. pdf (PDF, 505 KB)

Helmchen F, Kirchhoff F (2006) In vivo imaging of transgenic mice with fluorescent protein expression. In: Encyclopedic Reference of Genomics and Proteomics in Molecular Medicine, Springer Berlin Heidelberg, pp. 872-875.

Helmchen F, Nimmerjahn A (2006) Neue Einblicke ins Gehirn – Mikrogliazellverhalten bei Immunreaktionen Laborwelt 7: 30-32.

Helmchen F, Rudin M (2006) Functional imaging of the living brain – from fisheye to telezoom view. In: Neurotransmitter, Newsletter of the Swiss NCCR Neuro, No.7, pp. 1-3.


Helmchen F, and Denk W (2005) Deep tissue two-photon microscopy. Nature Methods, 2(12): 932-940. (Review) pdf (PDF, 599 KB)

Kerr JND, Greenberg D, and Helmchen F (2005) Imaging input and output of neocortical networks in vivo. Proc. Nat. Acad. Sci. USA, 102: 14063-14068. pdf (PDF, 10 MB)

Nimmerjahn A, Kirchhoff F, and Helmchen F (2005) Resting microglial cells are highly dynamic surveillants of brain parenchyma in vivo. Science, 308:1314-1318. pdf (PDF, 439 KB)

Sullivan MR, Nimmerjahn A, Sarkisov DV, Helmchen F, and Wang SSH (2005) In vivo calcium imaging of circuit activity in cerebellar cortex. Journal of Neurophysiology, 94: 1636-1644. pdf (PDF, 663 KB)

Helmchen F (2005) Calibration of fluorescent calcium indicators. In: Imaging in Neuroscience and Development: A Laboratory Manual (eds. Yuste R, Konnerth A), Cold Spring Harbor Laboratory Press.

Helmchen F, Tank DW (2005) A single compartment model of calcium dynamics in dendrites and nerve terminals. In: Imaging in Neuroscience and Development: A Laboratory Manual (eds. Yuste R, Konnerth A), Cold Spring Harbor Laboratory Press.

Helmchen F, Denk W (2005) A two-photon fiberscope for imaging in freely moving animals. In: Imaging in Neuroscience and Development: A Laboratory Manual (eds. Yuste R, Konnerth A), Cold Spring Harbor Laboratory Press.


Dittgen T, Nimmerjahn A, Komai S, Liczernski P, Waters J, Margrie TW, Helmchen F, Denk W, Brecht M, and Osten P (2004) Lentivirus-based genetic manipulations of cortical neurons and their optical and electrophysiological monitoring in vivo. Proc. Nat. Acad. Sci. USA, 101(52) : 18206-18211. pdf (PDF, 536 KB)


Waters J, and Helmchen F (2004) Boosting of action potential backpropagation by neocortical network activity in vivo. Journal of Neuroscience, 24(49) :11127-11136. pdf (PDF, 577 KB)

Brecht M, Fee MS, Garaschuk O, Helmchen F, Margrie TW, Svoboda K, and Osten P (2004). Novel approaches to monitor and manipulate single neurons in vivo. Journal of Neuroscience, 24(42):9223-9227. pdf (PDF, 236 KB)

Göbel W, Kerr NDJ, Nimmerjahn A, and Helmchen F (2004) Miniaturized twp-photon microscope based on a flexible coherent fiber bundle and a gradient-index lens objective. Optics Letters, 29(21) : 2521-2523.


Nimmerjahn A, Kirchhoff F, Kerr NDJ, and Helmchen F (2004) Sulforhodamine 101 as a specific marker of astroglia in the neocortex in vivo. Nature Methods, 1(1) : 31-37. pdf (PDF, 703 KB)

Broser PJ,, Schulte R, Roth A, Helmchen F, Waters J, Lang S, Sakmann B, and Wittum G (2004) Nonlinear anisotropic diffusion filtering of three-dimensional image data from 2-photon microscopy. Journal of Biomedical Optics, 9(6): 1253-1264.

Göbel W, Nimmerjahn A, Helmchen F (2004) Distortion-free delivery of femtosecond pulses from a Ti:sapphire laser through a hollow core photonic crystal fiber. Optics Letters, 29(11): 1285-1287.