Data, simulations and code at:

Original publication:

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

Code, examples and benchmark datasets at:

Original publication:
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. PDF



Original publication:
Boergens KM, Berning M, Bocklisch T, Braeunlein D, Drawitsch F, Frohnhofen J, Herold T, Otto P, Rzepka N, Werkmeister T, Werner D, Wiese G, Wissler H, Helmstaedter M (2017) webKnossos: efficient online 3D data annotation for connectomics, Nature Methods 14: 691-694. PDF


Code, examples and benchmark datasets at: 

Original publication:
Berning, M., Boergens, K.M. and Helmstaedter, M. (2015) SegEM: Efficient Image Analysis for High-Resolution Connectomics. Neuron 87: 1193-1206 (cover article)


RESCOP Skeleton Consolidation (2011, 2015)

For algorithm and backround, see Helmstaedter et al., 2011.

A more recent implementation (used in Hua et al., 2015) can be found here:
Supplementary Software in Hua et al., 2015

1 additional matlab file required for execution:


Skeleton Files (.nml format)


Original publications:
Helmstaedter, M, Briggmann KL, Denk W (2011): High-accuracy neurite reconstruction for high-throughput neuroanatomy. Nature Neuroscience 14:1081-1088 featured in “High-throughput anatomy: Charting the brain's networks.” Nature Neuroscience 490:293–298  PDF

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

Raw data, code, reconstructions at:

Original publication:
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: 168-174  PDF


Thalamocortical Innervations (2010)

Tool for extracting 1-dimensional innervation densitiy maps:

Original publication:
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 PDF

Numerical Simulations of Interneurons from L2/3 of Rat Somatosensory Cortex (2008)

  • Helmstaedter et al., 2008a,b: Reconstructions of L2/3 interneurons (.asc files):
  • Helmstaedter et al., 2008b: Numerical model of firing patterns in L2/3 interneurons:
  • Original publications
    • Helmstaedter M, Sakmann B, Feldmeyer D (2008a) Neuronal Correlates of Local and Translaminar Inhibtion with Reference to Cortical Columns, Cerebral Cortex doi: 10.1093/cercor/bhn141 PDF
    • Helmstaedter M, Sakmann B, Feldmeyer D (2008b) The Relation between Dendritic Geometry, Eletrical Excitability and Axonal Projections of L2/3 Interneurons in Rat Barrel Cortex, Cerebral Cortex doi: 10.1093/cercor/bhn138 PDF
    • Helmstaedter M, Sakmann B, Feldmeyer D (2008c) L2/3 Interneuron Groups Defines by Multiparameter Analysis of Axonal Projection, Dendritic Geometry and Eletrical Excitability, Cerebral Cortex doi: 10.1093/cercor/bhn130 PDF
    • Helmstaedter M, Staiger JF, Sakmann B, Feldmeyer D (2008d) Efficient Recruitment of Layer 2/3 Interneurons by Layer 4 Input in Single Columns of Rat Somatosensory Cortex, The Journal of Neuroscience 28(33):8273–8284 PDF
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