Publications of Winfried Denk

Journal Article (110)

2022
Journal Article
Kornfeld, J.; Januszewski, M.; Schubert, P. J.; Jain, V.; Denk, W.; Fee, M. S.: An anatomical substrate of credit assignment in reinforcement learning. bioRxiv (2022)
Journal Article
Svara, F. N.; Förster, D.; Kubo, F.; Januszewski, M.; Dal Maschio, M.; Schubert, P. J.; Kornfeld, J.; Wanner, A. A.; Laurell, E.; Denk, W. et al.; Baier, H.: Automated synapse-level reconstruction of neural circuits in the larval zebrafish brain. Nature Methods 19 (11), pp. 1357 - 1366 (2022)
2020
Journal Article
Abbott, L. F.; Bock, D. D.; Callaway, E. M.; Denk, W.; Dulac, C.; Fairhall, A. L.; Fiete, I.; Harris, K. M.; Helmstaedter, M.; Jain, V. et al.; Kasthuri, N.; LeCun, Y.; Lichtman, J. W.; Littlewood, P. B.; Luo, L.; Maunsell, J. H. R.; Reid, R. C.; Rosen, B. R.; Rubin, G. M.; Sejnowski, T. J.; Seung, H. S.; Svoboda, K.; Tank, D. W.; Tsao, D.; Van Essen, D. C.: The mind of a mouse. Cell 182 (6), pp. 1372 - 1376 (2020)
2018
Journal Article
Boergens, K. M.; Kapfer, C.; Helmstaedter, M.; Denk, W.; Borst, A.: Full reconstruction of large lobula plate tangential cells in Drosophila from a 3D EM dataset. PLoS One 13 (11), e0207828 (2018)
Journal Article
Januszewski, M.; Kornfeld, J.; Li, P. H.; Pope, A.; Blakely, T.; Lindsey, L.; Maitin-Shepard, J.; Tyka, M.; Denk, W.; Jain, V.: High-precision automated reconstruction of neurons with flood-filling networks. Nature Methods 15 (8), pp. 605 - 610 (2018)
Journal Article
Kornfeld, J.; Denk, W.: Progress and remaining challenges in high-throughput volume electron microscopy. Current Opinion in Neurobiology 50, pp. 261 - 267 (2018)
Journal Article
Svara, F.; Kornfeld, J.; Denk, W.; Bollmann, J. H.: Volume EM reconstruction of spinal cord reveals wiring specificity in speed-related motor circuits. Cell Reports 23 (10), pp. 2942 - 2954 (2018)
2017
Journal Article
Kornfeld, J.; Benezra, S. E.; Narayanan, R. T.; Svara, F.; Egger, R.; Oberlaender, M.; Denk, W.; Long, M. A.: EM connectomics reveals axonal target variation in a sequence-generating network. eLife 6, e24364 (2017)
Journal Article
Rickgauer, J. P.; Grigorieff, N.; Denk, W.: Single-protein detection in crowded molecular environments in cryo-EM images. eLife 6, e25648 (2017)
2015
Journal Article
Mikula, S.; Denk, W.: High-resolution whole-brain staining for electron microscopic circuit reconstruction. Nature Methods 12 (6), pp. 541 - 546 (2015)
2014
Journal Article
Kim, J. S.; Greene, M. J.; Zlateski, A.; Lee, K.; Richardson, M.; Turaga, S. C.; Purcaro, M.; Balkam, M.; Robinson, A.; Behabadi, B. F. et al.; Campos, M.; Denk, W.; Seung, H. S.; EyeWirers: Space-time wiring specificity supports direction selectivity in the retina. Nature 509 (7500), pp. 331 - 336 (2014)
2013
Journal Article
Binding, J.; Mikula, S.; Denk, W.: Low-dosage maximum-a-posteriori focusing and stigmation. Microscopy and Microanalysis 19 (1), pp. 38 - 55 (2013)
Journal Article
Helmchen, F.; Denk, W.; Kerr, J. N.: Miniaturization of two-photon microscopy for imaging in freely moving animals. Cold Spring Harbor Protocols 2013 (10), pp. 904 - 913 (2013)
Journal Article
Helmstaedter, M.; Briggman, K.; Turaga, S. C.; Jain, V.; Seung, H. S.; Denk, W.: Connectomic reconstruction of the inner plexiform layer in the mouse retina. Nature 500 (7461), pp. 168 - 174 (2013)
Journal Article
Titze, B.; Denk, W.: Automated in-chamber specimen coating for serial block-face electron microscopy. Journal of Microscopy 250 (2), pp. 101 - 110 (2013)
2012
Journal Article
Andres, B.; Koethe, U.; Kroeger, T.; Helmstaedter, M.; Briggman, K.; Denk, W.; Hamprecht, F. A.: 3D segmentation of SBFSEM images of neuropil by a graphical model over supervoxel boundaries. Medical Image Analysis 16 (4), pp. 796 - 805 (2012)
Journal Article
Bargmann, C.; Denk, W.; Graybiel, A.: An interview with...: The Kavli prize winners. Nature Reviews Neuroscience 13 (10), pp. 669 - 673 (2012)
Journal Article
Denk, W.; Briggman, K.; Helmstaedter, M.: Structural neurobiology: Missing link to a mechanistic understanding of neural computation. Nature Reviews Neuroscience 13 (5), pp. 351 - 358 (2012)
Journal Article
Denk, W.; Miesenböck, G.: Neurotechnology: Summa technologiae. Current Opinion in Neurobiology 22 (1), pp. 1 - 2 (2012)
Journal Article
Mikula, S.; Binding, J.; Denk, W.: Staining and embedding the whole mouse brain for electron microscopy. Nature Methods 9 (12), pp. 1198 - 1201 (2012)
2011
Journal Article
Briggman, K.; Helmstaedter, M.; Denk, W.: Wiring specificity in the direction-selectivity circuit of the retina. Nature 471 (7337), pp. 183 - 188 (2011)
Journal Article
Helmstaedter, M.; Briggman, K.; Denk, W.: High-accuracy neurite reconstruction for high-throughput neuroanatomy. Nature Neuroscience 14 (8), pp. 1081 - 1088 (2011)
Journal Article
Kleinfeld, D.; Bharioke, A.; Blinder, P.; Bock, D. D.; Briggman, K.; Chklovskii, D. B.; Denk, W.; Helmstaedter, M.; Kaufhold, J. P.; Lee, W. A. et al.; Meyer, H. S.; Micheva, K. D.; Oberlaender, M.; Prohaska, S.; Reid, R. C.; Smith, S. J.; Takemura, S.; Tsai, P. S.; Sakmann, B.: Large-scale automated histology in the pursuit of connectomes. The Journal of Neuroscience 31 (45), pp. 16125 - 16138 (2011)
Journal Article
Lichtman, J. W.; Denk, W.: The big and the small: Challenges of imaging the brain's circuits. Science 334 (6056), pp. 618 - 623 (2011)
Journal Article
Mittmann, W.; Wallace, D. J.; Czubayko, U.; Herb, J.; Schaefer, A. T.; Looger, L. L.; Denk, W.; Kerr, J. N.: Two-photon calcium imaging of evoked activity from L5 somatosensory neurons in vivo. Nature Neuroscience 14 (8), pp. 1089 - 1093 (2011)
Journal Article
Theer, P.; Denk, W.; Sheves, M.; Lewis, A.; Detwiler, P. B.: Second-harmonic generation imaging of membrane potential with retinal analogues. Biophysical Journal 100 (1), pp. 232 - 242 (2011)
2010
Journal Article
Aguirre, A. D.; Sawinski, J.; Huang, S. W.; Zhou, C.; Denk, W.; Fujimoto, J. G.: High speed optical coherence microscopy with autofocus adjustment and a miniaturized endoscopic imaging probe. Optics Express 18 (5), pp. 4222 - 4239 (2010)
Journal Article
Turaga, S. C.; Murray, J. F.; Jain, V.; Roth, F.; Helmstaedter, M.; Briggman, K.; Denk, W.; Seung, H. S.: Convolutional networks can learn to generate affinity graphs for image segmentation. Neural computation 22 (2), pp. 511 - 538 (2010)
2009
Journal Article
Euler, T.; Hausselt, S.; Margolis, D. J.; Breuninger, T.; Castell, X.; Detwiler, P. B.; Denk, W.: Eyecup Scope - Optical recordings of light stimulus-evoked fluorescence signals in the retina. Pflügers Archiv: European Journal of Physiology 457 (6), pp. 1393 - 1414 (2009)
Journal Article
Jurrus, E.; Hardy, M.; Tasdizen, T.; Fletcher, P. T.; Koshevoy, P.; Chien, C.; Denk, W.; Whitaker, R.: Axon tracking in serial block-face scanning electron microscopy. Medical Image Analysis 13 (1), pp. 180 - 188 (2009)
Journal Article
Sawinski, J.; Haydon-Wallace, D. J.; Greenberg, D. S.; Grossmann, S.; Denk, W.; Kerr, J. N.: Visually evoked activity in cortical cells imaged in freely moving animals. Proceedings of the National Academy of Sciences of the United States of America 106 (46), pp. 19557 - 19562 (2009)
Journal Article
Yamahachi, H.; Marik, S. A.; McManus, J. N.; Denk, W.; Gilbert, C. D.: Rapid axonal sprouting and pruning accompany functional reorganization in primary visual cortex. Neuron 64 (5), pp. 719 - 729 (2009)
2008
Journal Article
Helmstaedter, M.; Briggman, K.; Denk, W.: 3D structural imaging of the brain with photons and electrons. Current Opinion in Neurobiology 18 (6), pp. 633 - 641 (2008)
Journal Article
Kerr, J. N.; Denk, W.: Imaging in vivo: Watching the brain in action. Nature Reviews Neuroscience 9 (3), pp. 195 - 205 (2008)
Journal Article
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 5 (1), pp. 61 - 67 (2008)
Journal Article
Kuhn, B.; Denk, W.; Bruno, R. M.: In vivo two−photon voltage−sensitive dye imaging reveals top−down control of cortical layers 1 and 2 during wakefulness. Proceedings of the National Academy of Sciences of the United States of America 105 (21), pp. 7588 - 7593 (2008)
Journal Article
Macke, J. H.; Maack, N.; Gupta, R.; Denk, W.; Schölkopf, B.; Borst, A.: Contour-propagation algorithms for semi-automated reconstruction of neural processes. Journal of Neuroscience Methods 167 (2), pp. 349 - 357 (2008)
Journal Article
Major, G.; Polsky, A.; Denk, W.; Schiller, J.; Tank, D. W.: Spatiotemporally graded NMDA spike/plateau potentials in basal dendrites of neocortical pyramidal neurons. Journal of Neurophysiology 99 (5), pp. 2584 - 2601 (2008)
Journal Article
O´Connell, M. K.; Murthy, S.; Phan, S.; Xu, C.; Buchanan, J.; Spilker, R.; Dalman, R. L.; Zarins, C. K.; Denk, W.; Taylor, C. A.: The three-dimensional micro- and nanostructure of the aortic medial lamellar unit measured using 3D confocal and electron microscopy imaging. Matrix Biology 27 (3), pp. 171 - 181 (2008)
Journal Article
Wallace, D. J.; Meyer zum Alten Borgloh, S.; Astori, S.; Yang, Y.; Bausen, M.; Kügler, S.; Palmer, A. E.; Tsien, R. Y.; Sprengel, R.; Kerr, J. N. et al.; Denk, W.; Hasan, M. T.: Single−spike detection in vitro and in vivo with a genetic Ca2+ sensor. Nature Methods 5 (9), pp. 797 - 804 (2008)
2007
Journal Article
Hausselt, S.; Euler, T.; Detwiler, P. B.; Denk, W.: A dendrite-autonomous mechanism for direction selectivity in retinal starburst amacrine cells. PLoS Biology 5 (7), 185, pp. 1474 - 1493 (2007)
Journal Article
Rückel, M.; Denk, W.: Properties of coherence-gated wavefront sensing. Journal of the Optical Society of America A 24 (11), pp. 3517 - 3529 (2007)
Journal Article
Sawinski, J.; Denk, W.: Miniature random-access fiber scanner for in vivo multiphoton imaging. Journal of Applied Physics 102 (3), 034701, pp. 1 - 8 (2007)
2006
Journal Article
Briggman, K.; Denk, W.: Towards neural circuit reconstruction with volume electron microscopy techniques. Current Opinion in Neurobiology 16 (5), pp. 562 - 570 (2006)
Journal Article
Komai, S.; Denk, W.; Osten, P.; Brecht, M.; Margrie, T. W.: Two-photon targeted patching (TPTP) in vivo. Nature Protocols 1 (2), pp. 648 - U5 (2006)
Journal Article
Komai, S.; Licznerski, P.; Cetin, A.; Waters, D. J.; Denk, W.; Brecht, M.; Osten, P.: Postsynaptic excitability is necessary for strengthening of cortical sensory responses during experience−dependent development. Nature Neuroscience 9 (9), pp. 1125 - 1133 (2006)
Journal Article
Rückel, M.; Mack-Bucher, J. A.; Denk, W.: Adaptive wavefront correction in two−photon microscopy using coherence gated wavefront sensing. Proceedings of the National Academy of Sciences of the United States of America 103 (46), pp. 17137 - 17142 (2006)
Journal Article
Stettler, D. D.; Yamahachi, H.; Li, W.; Denk, W.; Gilbert, C. D.: Axons and synaptic boutons are highly dynamic in adult visual cortex. Neuron 49 (6), pp. 877 - 887 (2006)
Journal Article
Theer, P.; Denk, W.: On the fundamental imaging−depth limit in two−photon microsopy. Journal of the Optical Society of America A 23 (12), pp. 3139 - 3149 (2006)
2005
Journal Article
Helmchen, F.; Denk, W.: Deep tissue two-photon microscopy. Nature Methods 2 (12), pp. 932 - 940 (2005)
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