Resources

 

SegEM (2015)
Methods for Automated Image Sementation in EM Based 
Connectomics

Code, examples and benchmark datasets at:
http://segem.brain.mpg.de/ 

Original publication:

 

 

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:
betainc_unnorm.m

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

 

 

Local Mouse Retina Connectome (2013)

Raw data, code, reconstructions at:

http://neuro.mpg.de/connectomics

Original publication:

 

 

Thalamocortical Innervations (2010)

Tool for extracting 1-dimensional innervation densitiy maps: 

rothko_v041.zip

Original publication:

 

 

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

 

Original publications: 

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