natverse packages

Core natverse

nat

NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons.

nat.nblast

Extends package 'nat' (NeuroAnatomy Toolbox) by providing a collection of NBLAST-related functions.

nat.templatebrains

Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.

catmaid

This package provide access to the API exposed by the CATMAID (C ollaborative A nnotation T oolkit for M assive A mounts of I mage D ata) web tool.

neuprintr

Access to the neuprint connectome analysis service, including functions to fetch skeletons, synapses and ROIs, query connectivity data and develop new low level queries.

drvid

API access to the 'DVID' (Distributed, Versioned, Image-oriented Dataservice).

neuromorphr

Access to the NeuroMorpho online repository (version 7.7 ) for single-cell neuron morphology data, enabling users to easily find and use neurons from this repository with nat family packages.

elmr

Provides tools to move between adult brain EM and light level data, emphasising the interaction between the CATMAID web application and the R Neuroanatomy Toolbox package.

nat.flybrains

Includes 3D brain surfaces, bridging and mirroring registrations, and neuropil segmentations for various template brains.

flycircuit

Functions and data for spatial analysis and annotation of neurons from the 'FlyCircuit' collection available online at http://flycircuit.tw.

nabor

An R wrapper for 'libnabo', an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D).

The natverse also includes many other packages with more specialised usage. They are not loaded automatically with library(natverse), so you’ll need to load each one with its own call to library().

External toolboxes

The following are the external toolboxes that play well with the natverse:

rgl

Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.).

igraph

Routines for simple graphs and network analysis.

alphashape3d

Implementation in R of the alpha-shape of a finite set of points in the three-dimensional space.

Rvcg

Operations on triangular meshes based on 'VCGLIB'.

Morpho

A toolset for Geometric Morphometrics and mesh processing.

Get help

If you’re asking for help, reporting a bug, or requesting a new feature, you’re more likely to succeed if you include a good reproducible example, which is precisely what the reprex package is meant for. You can learn more about reprex, along with other tips on how to help others help you in the help section.


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