Publications Helmstaedter

1.

Journal Article

Schmidt, M.; Motta , A.; Sievers, M.; Helmstaedter, M.: RoboEM: automated 3D flight tracing for synaptic-resolution connectomics. Nat Methods (2024)

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2.

Journal Article

Song, K.; Feng, Z.; Helmstaedter, M.: High-contrast en bloc staining of mouse whole-brain and human brain samples for EM-based connectomics. Nat. Methods (2023)

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3.

Journal Article

Hua, Y.; Loomba, S.; Pawlak, V.; Voit, K.-M.; Laserstein, P.; Boergens, K. M.; Wallace, D. J.; Kerr, J. N. D.; Helmstaedter, M.: Connectomic analysis of thalamus-driven disinhibition in cortical layer 4. Cell Reports 41 (2), 111476 (2022)

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4.

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Loomba, S.; Straehle, J.; Gangadharan, V.; Heike, N.; Khalifa, A.; Motta, A.; Ju, N.; Sievers, M.; Gempt, J.; Meyer, H. S. et al.; Helmstaedter, M.: Connectomic comparison of mouse and human cortex. Science 377 (6602), eabo0924 (2022)

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5.

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Klinger, E.; Motta, A.; Marr, C.; Theis , F. J.; Helmstaedter, M.: Cellular connectomes as arbiters of local circuit models in the cerebral cortex. Nature Communications 12, 2785 (2021)

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6.

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Karimi, A.; Odenthal, J.; Drawitsch, F.; Boergens, K. M.; Helmstaedter, M.: Cell-type specific innervation of cortical pyramidal cells at their apical dendrites. eLife 9, e46876 (2020)

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7.

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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)

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8.

Journal Article

Gour, A.; Boergens, K. M.; Heike, N.; Hua, Y.; Laserstein, P.; Song, K.; Helmstaedter, M.: Postnatal connectomic development of inhibition in mouse barrel cortex. Science 371 (6528) (2020)

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9.

Journal Article

Yuste, R.; Hawrylycz, M.; Aalling, N.; Aguilar-Valles, A.; Arendt, D.; Arnedillo, R. A.; Ascoli, G. A.; Bielza, C.; Bokharaie, V.; Bergmann, T. B. et al.; Bystron, I.; Capogna, M.; Chang, Y.; Clemens, A.; de Kock, C. P. J.; DeFelipe, J.; Dos Santos, S. E.; Dunville, K.; Feldmeyer, D.; Fiath, R.; Fishell, G. J.; Foggetti, A.; Gao, X.; Ghaderi, P.; Goriounova, N. A.; Gunturkun, O.; Hagihara, K.; Hall, V. J.; Helmstaedter, M.; Herculano, S.; Hilscher, M. M.; Hirase, H.; Hjerling-Leffler, J.; Hodge, R.; Huang, J.; Huda, R.; Khodosevich, K.; Kiehn, O.; Koch, H.; Kuebler, E. S.; Kuhnemund, M.; Larranaga, P.; Lelieveldt, B.; Louth, E. L.; Lui, J. H.; Mansvelder, H. D.; Marin, O.; Martinez-Trujillo, J.; Moradi Chameh, H.; Nath, A.; Nedergaard, M.; Nemec, P.; Ofer, N.; Pfisterer, U. G.; Pontes, S.; Redmond, W.; Rossier, J.; Sanes, J. R.; Scheuermann, R.; Serrano-Saiz, E.; Steiger, J. F.; Somogyi, P.; Tamas, G.; Tolias, A. S.; Tosches, M. A.; Garcia, M. T.; Vieira, H. M.; Wozny, C.; Wuttke, T. V.; Yong, L.; Yuan, J.; Zeng, H.; Lein, E.: A community-based transcriptomics classification and nomenclature of neocortical cell types. Nat Neurosci (2020)

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10.

Journal Article

Motta, A.; Schurr, M.; Staffler, B.; Helmstaedter, M.: Big data in nanoscale connectomicx, and the greed for training labels. Current Opinion in Neurobiology (55), pp. 180 - 187 (2019)

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Journal Article

Motta, A.; Berning, M.; Boergens, K. M.; Staffler, B.; Beining, M.; Loomba, S.; Hennig, P.; Wissler, H.; Helmstaedter, M.: Dense connectomic reconstruction in layer 4 of the somatosensory cortex. Science 366 (6469) (2019)

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12.

Journal Article

Drawitsch, F.; Karimi, A.; Boergens, K. M.; Helmstaedter, M.: FluoEM, virtual labeling of axons in three-dimensional electron microscopy data for long-range connectomics. eLife 14 (7), e38976 (2018)

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13.

Journal Article

Parag, T.; Berger, D.; Kamentsky, L.; Staffler, B.; Wei, D.; Helmstaedter, M.; Lichtman, J. W.; Pfister, H.: Detecting Synapse Location and Connectivity by Signed Proximity Estimation and Pruning with Deep Nets. arXiv preprint arXiv:1807.02739 (2018)

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Journal Article

Staffler, B.; Berning, M.; Boergens, K. M.; Gour, A.; van der Smagt, P.; Helmstaedter, M.: SynEM, automated synapse detection for connectomics. eLife 2017 (6), e26414 (2017)

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15.

Journal Article

Boergens, K. M.; Berning, M.; Bocklisch, T.; Braunlein, D.; Drawitsch, F.; Frohnhofen, J.; Herold, T.; Otto, P.; Rzepka, N.; Werkmeister, T. et al.; Werner, D.; Wiese, G.; Wissler, H.; Helmstaedter, M.: webKnossos: efficient online 3D data annotation for connectomics. Nat Methods 14 (7), pp. 691 - 694 (2017)

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16.

Journal Article

Schmidt, H.; Gour, A.; Straehle, J.; Boergens, K. M.; Brecht, M.; Helmstaedter, M.: Axonal synapse sorting in medial entorhinal cortex. Nature 549 (7673), pp. 469 - 475 (2017)

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17.

Journal Article

Amit, I.; Baker, D.; Barker, R.; Berger, B.; Bertozzi, C.; Bhatia, S.; Biffi, A.; Demichelis, F.; Doudna, J.; Dowdy, S. F. et al.; Endy, D.; Helmstaedter, M.; Junca, H.; June, C.; Kamb, S.; Khvorova, A.; Kim, D. H.; Kim, J. S.; Krishnan, Y.; Lakadamyali, M.; Lappalainen, T.; Lewin, S.; Liao, J.; Loman, N.; Lundberg, E.; Lynd, L.; Martin, C.; Mellman, I.; Miyawaki, A.; Mummery, C.; Nelson, K.; Paz, J.; Peralta-Yahya, P.; Picotti, P.; Polyak, K.; Prather, K.; Qin, J.; Quake, S.; Regev, A.; Rogers, J. A.; Shetty, R.; Sommer, M.; Stevens, M.; Stolovitzky, G.; Takahashi, M.; Tang, F.; Teichmann, S.; Torres-Padilla, M. E.; Tripathi, L.; Vemula, P.; Verdine, G.; Vollmer, F.; Wang, J.; Ying, J. Y.; Zhang, F.; Zhang, T.: Voices of biotech. Nat Biotechnol 34 (3), pp. 270 - 275 (2016)

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18.

Journal Article

Berning, M.; Boergens, K. M.; Helmstaedter, M.: SegEM: Efficient Image Analysis for High-Resolution Connectomics. Neuron 87 (6), pp. 1193 - 1206 (2015)

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19.

Journal Article

Borst, A.; Helmstaedter, M.: Common circuit design in fly and mammalian motion vision. Nat Neurosci 18 (8), pp. 1067 - 1076 (2015)

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20.

Journal Article

Helmstaedter, M.: The mutual inspirations of machine learning and neuroscience. Neuron 86 (1), pp. 25 - 28 (2015)

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21.

Journal Article

Hoffmann, J. H.; Meyer, H. S.; Schmitt, A. C.; Straehle, J.; Weitbrecht, T.; Sakmann, B.; Helmstaedter, M.: Synaptic Conductance Estimates of the Connection Between Local Inhibitor Interneurons and Pyramidal Neurons in Layer 2/3 of a Cortical Column. Cereb Cortex 25 (11), pp. 4415 - 4429 (2015)

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22.

Journal Article

Hua, Y.; Laserstein, P.; Helmstaedter, M.: Large-volume en-bloc staining for electron microscopy-based connectomics. Nat Commun 6, 7923 (2015)

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23.

Journal Article

Koelbl, C.; Helmstaedter, M.; Lubke, J.; Feldmeyer, D.: A barrel-related interneuron in layer 4 of rat somatosensory cortex with a high intrabarrel connectivity. Cerebral Cortex 25 (3), pp. 713 - 725 (2015)

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24.

Journal Article

Helmstaedter, M.: Cellular-resolution connectomics: challenges of dense neural circuit reconstruction. Nat Methods 10 (6), pp. 501 - 7 (2013)

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25.

Journal Article

Helmstaedter, M.; Briggman, K. L.; 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 - 74 (2013)

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26.

Journal Article

Egger, R.; Narayanan, R. T.; Helmstaedter, M.; de Kock, C. P.; Oberlaender, M.: 3D reconstruction and standardization of the rat vibrissal cortex for precise registration of single neuron morphology. PLoS Comput Biol 8 (12), e1002837 (2012)

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27.

Journal Article

Andres, B.; Koethe, U.; Kroeger, T.; Helmstaedter, M.; Briggman, K. L.; Denk, W.; Hamprecht, F. A.: 3D segmentation of SBFSEM images of neuropil by a graphical model over supervoxel boundaries. Med Image Anal 16 (4), pp. 796 - 805 (2012)

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28.

Journal Article

Denk, W.; Briggman, K. L.; Helmstaedter, M.: Structural neurobiology: missing link to a mechanistic understanding of neural computation. Nat Rev Neurosci 13 (5), pp. 351 - 8 (2012)

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29.

Journal Article

Helmstaedter, M.; Mitra, P. P.: Computational methods and challenges for large-scale circuit mapping. Curr Opin Neurobiol 22 (1), pp. 162 - 9 (2012)

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30.

Journal Article

Oberlaender, M.; de Kock, C. P.; Bruno, R. M.; Ramirez, A.; Meyer, H. S.; Dercksen, V. J.; Helmstaedter, M.; Sakmann, B.: Cell type-specific three-dimensional structure of thalamocortical circuits in a column of rat vibrissal cortex. Cereb Cortex 22 (10), pp. 2375 - 91 (2012)

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31.

Journal Article

Briggman, K. L.; Helmstaedter, M.; Denk, W.: Wiring specificity in the direction-selectivity circuit of the retina. Nature 471 (7337), pp. 183 - 8 (2011)

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32.

Journal Article

Helmstaedter, M.; Briggman, K. L.; Denk, W.: High-accuracy neurite reconstruction for high-throughput neuroanatomy. Nat Neurosci 14 (8), pp. 1081 - 8 (2011)

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33.

Journal Article

Kleinfeld, D.; Bharioke, A.; Blinder, P.; Bock, D. D.; Briggman, K. L.; Chklovskii, D. B.; Denk, W.; Helmstaedter, M.; Kaufhold, J. P.; Lee, W. C. 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. J Neurosci 31 (45), pp. 16125 - 38 (2011)

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34.

Journal Article

Meyer, H. S.; Schwarz, D.; Wimmer, V. C.; Schmitt, A. C.; Kerr, J. N.; Sakmann, B.; Helmstaedter, M.: Inhibitory interneurons in a cortical column form hot zones of inhibition in layers 2 and 5A. Proc Natl Acad Sci U S A 108 (40), pp. 16807 - 12 (2011)

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35.

Journal Article

Meyer, H. S.; Wimmer, V. C.; Hemberger, M.; Bruno, R. M.; de Kock, C. P.; Frick, A.; Sakmann, B.; Helmstaedter, M.: Cell type-specific thalamic innervation in a column of rat vibrissal cortex. Cereb Cortex 20 (10), pp. 2287 - 303 (2010)

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36.

Journal Article

Meyer, H. S.; Wimmer, V. C.; Oberlaender, M.; de Kock, C. P.; Sakmann, B.; Helmstaedter, M.: Number and laminar distribution of neurons in a thalamocortical projection column of rat vibrissal cortex. Cereb Cortex 20 (10), pp. 2277 - 86 (2010)

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37.

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 Comput 22 (2), pp. 511 - 38 (2010)

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38.

Journal Article

Helmstaedter, M.; Sakmann, B.; Feldmeyer, D.: L2/3 interneuron groups defined by multiparameter analysis of axonal projection, dendritic geometry, and electrical excitability. Cereb Cortex 19 (4), pp. 951 - 62 (2009)

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39.

Journal Article

Helmstaedter, M.; Sakmann, B.; Feldmeyer, D.: The relation between dendritic geometry, electrical excitability, and axonal projections of L2/3 interneurons in rat barrel cortex. Cereb Cortex 19 (4), pp. 938 - 50 (2009)

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40.

Journal Article

Helmstaedter, M.; Sakmann, B.; Feldmeyer, D.: Neuronal correlates of local, lateral, and translaminar inhibition with reference to cortical columns. Cereb Cortex 19 (4), pp. 926 - 37 (2009)

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41.

Journal Article

Frick, A.; Feldmeyer, D.; Helmstaedter, M.; Sakmann, B.: Monosynaptic connections between pairs of L5A pyramidal neurons in columns of juvenile rat somatosensory cortex. Cereb Cortex 18 (2), pp. 397 - 406 (2008)

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42.

Journal Article

Helmstaedter, M.; Briggman, K. L.; Denk, W.: 3D structural imaging of the brain with photons and electrons. Curr Opin Neurobiol 18 (6), pp. 633 - 41 (2008)

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43.

Journal Article

Helmstaedter, M.; Staiger, J. F.; Sakmann, B.; Feldmeyer, D.: Efficient recruitment of layer 2/3 interneurons by layer 4 input in single columns of rat somatosensory cortex. J Neurosci 28 (33), pp. 8273 - 84 (2008)

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44.

Journal Article

Petilla Interneuron Nomenclature, G.; Ascoli, G. A.; Alonso-Nanclares, L.; Anderson, S. A.; Barrionuevo, G.; Benavides-Piccione, R.; Burkhalter, A.; Buzsaki, G.; Cauli, B.; Defelipe, J. et al.; Fairen, A.; Feldmeyer, D.; Fishell, G.; Fregnac, Y.; Freund, T. F.; Gardner, D.; Gardner, E. P.; Goldberg, J. H.; Helmstaedter, M.; Hestrin, S.; Karube, F.; Kisvarday, Z. F.; Lambolez, B.; Lewis, D. A.; Marin, O.; Markram, H.; Munoz, A.; Packer, A.; Petersen, C. C.; Rockland, K. S.; Rossier, J.; Rudy, B.; Somogyi, P.; Staiger, J. F.; Tamas, G.; Thomson, A. M.; Toledo-Rodriguez, M.; Wang, Y.; West, D. C.; Yuste, R.: Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex. Nat Rev Neurosci 9 (7), pp. 557 - 68 (2008)

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45.

Journal Article

Helmstaedter, M.; de Kock, C. P.; Feldmeyer, D.; Bruno, R. M.; Sakmann, B.: Reconstruction of an average cortical column in silico. Brain Res Rev 55 (2), pp. 193 - 203 (2007)

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46.

Journal Article

Schaefer, A. T.; Helmstaedter, M.; Schmitt, A. C.; Bar-Yehuda, D.; Almog, M.; Ben-Porat, H.; Sakmann, B.; Korngreen, A.: Dendritic voltage-gated K+ conductance gradient in pyramidal neurones of neocortical layer 5B from rats. J Physiol 579 (Pt 3), pp. 737 - 52 (2007)

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47.

Journal Article

Schaefer, A. T.; Helmstaedter, M.; Sakmann, B.; Korngreen, A.: Correction of conductance measurements in non-space-clamped structures: 1. Voltage-gated K+ channels. Biophys J 84 (6), pp. 3508 - 28 (2003)

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Publications

Journal Article (47)

Book Chapter (2)