Resources

Data Repository at: 
l4dense2019.brain.mpg.de Original publication: Motta A, Berning M, Boergens KM, Staffler B,  Beining M, Loomba S, Hennig P,  Wissler H,  Helmstaedter M (2019) Dense connectomic reconstruction in layer 4 of the somatosensory cortex. Science, doi: 10.1126/science.aay3134. PDF more

Data, simulations and code at: 
http://plass.brain.mpg.de/ 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: 
http://synem.brain.mpg.de/ 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 more

See http://webknossos.org 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 more

Code, examples and benchmark datasets at:
http://segem.brain.mpg.de/  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)
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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:
betainc_unnorm (.m format)
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: http://neuro.mpg.de/connectomics 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 more

Tool for extracting 1-dimensional innervation densitiy maps:  rothko_v041.zip 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

• Helmstaedter et al., 2008a,b: Reconstructions of L2/3 interneurons (.asc files):
  
  • Dendrites and Axons (n=51) 7.3MB 
  • Dendrites (n=57) 1.2MB 
  • L2/3 pyramidal neurons as control (n=4) 0.3MB
    
• Helmstaedter et al., 2008b: Numerical model of firing patterns in L2/3 interneurons:
  
  • All Model Data (1MB)
  • README.pdf (40KB)
• 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