MPI Brain

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. (December 3, 2020) DOI: 10.1126/science.abb4534

Motta A, Schurr M, Staffler B, Helmstaedter M (2019), Big data in nanoscale connectomics, and the greed for training labels,  ScienceDirect

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

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Drawitsch F, Karimi A, Boergens KM, Helmstaedter M (2018) FluoEM, virtual labeling of axons in 3-dimensional electron microscopy data for long-range connectomics, eLife DOI:10.7554/eLife.38976 Pubmed pdf

Kubota Y, Sohn J, Hatada S, Schurr M, Straehle J, Gour A, Neujahr R, Miki T, Mikula S, Kawaguchi Y (2018) A carbon nanotube tape for serial-section electron microscopy of brain ultrastructure, Nature Communications 9:437. Pubmed pdf 

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

Boergens KM, Berning M, Bocklisch T, Braeunlein D, Drawitsch F, Frohnhofen J, Herold T, Otto P, Rzepka N, Werkmeister DW, Werner D, Wiese G, Wissler H, Helmstaedter M (2017) webKnossos: Efficient Online 3D Data Annotation for Connectomics, Nature Methods 14:691-694. Pubmed pdf

Staffler B, Berning M, Boergens KM, Gour A, van der Smagt P, Helmstaedter M (2017) SynEM, automated synapse detection for connectomics, eLife, doi: 10.755/eLife.26414. Pubmed pdf 

Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M et al. (2016) Voices of Biotech, Nature Biotechnology 34:270-275. Pubmed pdf

Berning M, Boergens KM, Helmstaedter, M (2015) SegEM: Efficient Image Analysis for High-Resolution Connectomics, Neuron 87:1193–1206. (cover article) News Pubmed pdf

Borst A, Helmstaedter M (2015) Common Circuit Design in Fly and Mammalian Motion Vision, Nature Neuroscience 18:1067-76. Pubmed pdf

Helmstaedter M (2015) The Mutual Inspirations of Machine Learning and Neuroscience, Neuron 86:25-8. Pubmed pdf

Hoffmann JH, Meyer HS, Schmitt AC, Straehle J, Weitbrecht T, Sakmann B, Helmstaedter M. (2015) Synaptic Conductance Estimates of the Connection Between Local Inhibitor Interneurons and Pyramidal Neurons in Layer 2/3 of a Cortical Column, Cerebral Cortex 10:4451-29. Pubmed pdf

Hua Y, Laserstein P, Helmstaedter M (2015) Large-Volume en-bloc Staining for Electron Microscopy-Based Connectomics, Nature Communications 6:7923. Pubmed pdf

Koelbl C, Helmstaedter M, Luebke J, Feldmeyer D (2015) A Barrel-Related Interneuron in Layer 4 of Rat Somatosensory Cortex with a High Intrabarrel Connectivity, Cerebral Cortex 25:713-25. Pubmed pdf

Helmstaedter M, Briggman KL, Turaga SC, Jain V, Seung HS, Denk W (2013) Connectomic Reconstruction of the Inner Plexiform Layer in the Mouse Retina, Nature 500:168-74. Pubmed pdf

Helmstaedter M (2013) Cellular-Resolution Connectomics: Challenges of Dense Neural Circuit Reconstruction, Nature Methods 10:501-7.Pubmed  pdf

Andres B, Koethe U, Kroeger T, Helmstaedter M, Briggman KL, Denk W, Hamprecht FA (2012) 3D Segmentation of SBFSEM Images of Neuropil by a Graphical Model over Supervoxel Boundaries, Medical Image Analysis 16:796-805. Pubmed pdf

Egger R, Narayanan RT, Helmstaedter M, de Kock CP, Oberlaender M (2012) 3D Reconstruction and Standardization of the Rat Vibrissal Cortex for Precise Registration of Single Neuron Morphology, PLOS Computational Biology 8. Pubmed pdf

Denk W, Briggman KL, Helmstaedter M (2012) Structural Neurobiology: Missing Link to a Mechanistic Understanding of Neural Computation, Nature Reviews Neuroscience 13:351-358. Pubmed  pdf

Helmstaedter M, Mitra PP (2012) Computational Methods and Challenges for lLrge-Scale Circuit Mapping, Current Opinion in Neurobiology 22:162-9. Pubmed pdf

Oberlaender M, de Kock CP, Bruno RM, Ramirez A, Meyer HS, Dercksen VJ, Helmstaedter M, Sakmann B (2012) Cell Type-Specific Three-Dimensional Structure of Thalamocortical Circuits in a Column of Rat Vibrissal Cortex, Cerebral Cortex 22:2375-91. Pubmed pdf

Briggman KL, Helmstaedter M, Denk W (2011) Wiring Specificity in the Direction-Selectivity Circuit of the Retina, Nature 471:183-8. Pubmed pdf

Helmstaedter M, Briggman KL, Denk W (2011) High-Accuracy Neurite Reconstruction for High-Throughput Neuroanatomy, Nature Neuroscience 14:1081-88. Pubmed pdf

Kleinfeld D, Bharioke A, Blinder P, Bock DD, Briggman KL, Chklovskii DB, Denk W, Helmstaedter M et al. (2011) Large-Scale Automated Histology in the Pursuit of Connectomes, Journal of Neuroscience 31:16125-38. Pubmed pdf

Meyer HS, Schwarz D, Wimmer VC, Schmitt AC, Kerr JN, Sakmann B, Helmstaedter M (2011) Inhibitory Interneurons in a Cortical Column form Hot Zones of Inhibition in Layers 2 and 5A, Proceedings of the National Academy of Sciences (PNAS) 108:16807-12. Pubmed pdf

Meyer HS, Wimmer VC, Hemberger M, Bruno RM, de Kock CP, Frick A, Sakmann B, Helmstaedter M (2010) Cell Type-Specific Thalamic Innervation in a Column of Rat Vibrissal Cortex, Cerebral Cortex 20:2287-303 (Cover article). Pubmed pdf

Meyer HS, Wimmer VC, Oberlaender M, de Kock CP, Sakmann B, Helmstaedter M (2010) Number and Laminar Distribution of Neurons in a Thalamocortical Projection Column of Rat Vibrissal Cortex, Cerebral Cortex 20:2277-86. Pubmed pdf

Turaga SC, Murray JF, Jain V, Roth F, Helmstaedter M, Briggman KL, Denk W, Seung HS (2010) Convolutional Networks Can Learn to Generate Affinity Graphs for Image Segmentation, Neural Computation 22:511-38. Pubmed pdf

Helmstaedter M, Sakmann B, Feldmeyer D (2009) L2/3 Interneuron Groups Defined by Multiparameter Analysis of Axonal Projection, Dendritic Geometry and Electrical Excitability, Cerebral Cortex 19:951-62. Pubmed pdf  Additional resources

Helmstaedter M, Sakmann B, Feldmeyer D (2009) The Relation Between Dendritic Geometry, Electrical Excitability and Axonal Projections of L2/3 Interneurons in Rat Barrel Cortex. Cerebral Cortex 19:938-50. Pubmed pdf  Additional resources

Helmstaedter M, Sakmann B, Feldmeyer D (2009) Neuronal Correlates of Local, Lateral and Translaminar Inhibition with Reference to Cortical Columns, Cerebral Cortex 19:926-37. (Cover article) Pubmed pdf  Additional resources

Helmstaedter M, Briggman KL, Denk W (2008) 3D Structural Imaging of the Brain with Photons and Electrons, Current Opinion in Neurobiology 18(6):633-41. Pubmed pdf

Helmstaedter M, Staiger JF, Sakmann B, Feldmeyer D (2008) Efficient Recruitment of Layer 2/3 Interneurons by Layer 4 Input in Single Columns of Rat Somatosensory Cortex, Journal of Neuroscience 28(13):8273-8284. Pubmed pdf additional resources

Ascoli GA, Alonso-Nanclares L, Anderson SA, Barrionuevo G, Benavides-Piccione R, Burkhalter A, Buzsaki G, Cauli B, Defelipe J, Fairen A, Feldmeyer D, Fishell G, Fregnac Y, Freund TF, Gardner D, Gardner EP, Goldberg JH, Helmstaedter M, Hestrin S, Karube F, Kisvarday ZF, Lambolez B, Lewis DA, Marin O, Markram H, Munoz A, Packer A, Petersen CC, Rockland KS, Rossier J, Rudy B, Somogyi P, Staiger JF, Tamas G, Thomson AM, Toledo-Rodriguez M, Wang Y, West DC, Yuste R (2008) Petilla Terminology: Nomenclature of Features of GABAergic Interneurons of the Cerebral Cortex, Nature Reviews Neuroscience 9(7):557-568. Pubmed pdf

Frick A, Feldmeyer D, Helmstaedter M, Sakmann B (2008) Monosynaptic Connections Between Pairs of L5A Pyramidal Neurons in Columns of Juvenile Rat Somatosensory Cortex, Cerebral Cortex 18(2):397-406. Pubmed pdf

Helmstaedter M, de Kock CP, Feldmeyer D, Bruno RM, Sakmann B (2007) Reconstruction of an Average Cortical Column in Silico, Brain Research Reviews 55(2):193-203. Pubmed pdf

Schaefer AT*, Helmstaedter M*, Schmitt AC, Bar-Yehuda D, Almog M, Ben-Porat H, Sakmann B, Korngreen A (2007) Dendritic Voltage-Gated K+ Conductance Gradient in Pyramidal Neurones of Neocortical Layer 5B from Rats, Journal of Physiology 579(3):737-52. *equally contributing Pubmed pdf

Schaefer AT, Helmstaedter M, Sakmann B, Korngreen A (2003) Correction of Conductance Measurements in non-space-clamped Structures: 1. Voltage-gated K+ Channels, Biophysical Journal 84(6):3508-528. Pubmed pdf