Code Repository for

Dense Connectomic Reconstruction in Layer 4 of the Somatosensory Cortex
Alessandro Motta*, Manuel Berning*, Kevin M. Boergens*, Benedikt Staffler*, Marcel Beining, Sahil Loomba, Philipp Hennig, Heiko Wissler, Moritz Helmstaedter. Science (2019). DOI: 10.1126/science.aay3134

with code contributions from Florian Drawitsch, Ali Karimi, Martin Schmidt, Christian Schramm, Martin Zauser, and more.

The electron microscopy volume, neurite reconstructions, and more are available

• for viewing and annotation at webknossos.org, and
• for download at https://l4dense2019.brain.mpg.de.

Getting Started

The code in this repository was primarily developed for the R2015b and R2017b releases of MATLAB.

To run the code, first download the ZIP archive or clone this repository using Git. Then install the external dependencies listed below. Finally, switch to the code directory and start MATLAB. This should automatically run the startup.m script.

A high-level commentary on all the processing performed in this work is available in the main and supplementary methods.

Dependencies

• JSONLab
• JSON-C
• MATLAB JSON
• GPML
• WKW
• DGof
  Taylor B. Arnold, John W. Emerson (2011) The R Journal
  Nonparametric Goodness-of-Fit Tests for Discrete Null Distributions
  DOI: 10.32614/RJ-2011-016

Acknowledgements

• Dr. Zdravko Botev for kde2d, a function for fast two-dimensional kernel density estimation
  Z. I. Botev, J. F. Grotowski, D. P. Kroese (2010) Annals of Statistics
  Kernel Density Estimation via Diffusion
  DOI: 10.1214/10-AOS799
• Kevin L. Briggman for early versions of the 3D image alignment routines that were used in
  Kevin L. Briggman, Moritz Helmstaedter, Winfried Denk (2011) Nature
  Wiring Specificity in the Direction-selectivity Circuit of the Retina
  DOI: 10.1038/nature09818
• Timothy E. Holy for distinguishable_colors, a function to "generate maximally perceptually-distinct colors"
• Arseny Kapoulkine for pugixml, a XML parser library for C++
  https://pugixml.org/

License

This project is licensed under the MIT license.
Copyright (c) 2019 Department of Connectomics, Max Planck Institute for Brain Research, D-60438 Frankfurt am Main, Germany