Package OverviewProvides an overview of key functions and classes 


Neuron similarity, search and clustering tools 

Key functionsThe main entry points to neuron search and clustering 

Calculate similarity score for neuron morphologies 

Wrapper function to compute all by all NBLAST scores for a set of neurons 

Cluster a set of neurons 

Plotting resultsVisualise pairwise neuron search or clustering results 

Methods to identify and plot groups of neurons cut from an 

Display two neurons with segments in the query coloured by similarity 

Return the labels of items in 1 or more groups cut from hclust object 

Scoring MatricesCalculate the scoring matrices that define NBLAST similarity 

Create a scoring matrix given matching and nonmatching sets of neurons 

Calculate scoring matrix from probability matrices for matching and nonmatching sets of neurons 

Calculate probability matrix from distances and dot products between neuron segments 

Calculate distances and dot products between two sets of neurons 

Scoring matrices for neuron similarities in FCWB template brain 

Mid level functions for result matricesFunctions that you might use to manipulate matrices containing all by all NBLAST results for use with other clustering strategies (besides nhclust) 

Return scores (or distances) for given query and target neurons 

Convert (a subset of) a raw score matrix to a distance matrix 

Convert a subset of a square score matrix to a sparse representation 

Low level search functionsIntended for developer use 

Produce similarity score for neuron morphologies 

Utility function to generate all or random pairs of neurons 

Compute point & tangent vector similarity score between two linesets 

20 traced Drosophila neurons from Chiang et al 2011 

Matrix utility functionsIntended for developer use 

Extract diagonal terms from a variety of matrix types 


Extract parts of a sparse 
Add one or more submatrices to a sparse score matrix 

Add forwards, reverse and self scores for a pair of neurons to a sparse score matrix 