Publications

1.

Journal Article

Schmidt, M.; Motta, A.; Sievers, M.; Helmstaedter, M.: RoboEM: automated 3D flight tracing for synaptic-resolution connectomics. Nat Methods 21, pp. 908 - 913 (2024)

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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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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.

Journal Article

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.

Journal Article

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.

Journal Article

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.

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)

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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)