Elegance

Elegance code on Github

Elegance is a program designed and used by the Emmons laboratory for rapid annotation of electron micrographs for connectomics. It generates skeleton diagrams of neurons, synapse lists, and adjacency matrices. It stores the annotation data in MySQL tables. It is described in this publication: Xu M, Jarrell TA, Wang Y, Cook SJ, Hall DH, et al. (2013) Computer Assisted Assembly of Connectomes from Electron Micrographs: Application to Caenorhabditis elegans. PLoS ONE 8(1): e54050.
doi:10.1371/journal.pone.0054050
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0054050.
It was used for the reconstructions described in Jarrell et al., 2013 and Cook et al., 2019.

MATLAB routines for analysis of connectomes, by Adam Bloniarz, Google

Adjacency and Similarity Matrix MATLAB Scripts [zip]

AdjacencyMatrix, SimilarityMatrix, and MatrixComparison are MATLAB programs for analysis of connectome connectivity tables. They convert CSV files into MATLAB format and allow for simple manipulation of the matrices, such as adding them together or multiplying by a constant, combining neurons into groups, analysis of graph properties such as degree distribution, modularity, and so forth, and comparison of connectivity of neurons. For complete lists of functions, consult the first page of each guide.

C. elegans connectome tables in MATLAB-ready format, by Kamal Premaratne, University of Miami

Supplementary Information 5 of Cook et al., 2019. Excel connectivity tables in MATLAB-ready format. [zip]