nat - NeuroAnatomy Toolbox for Analysis of 3D Image Data

NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).

Last updated 1 months ago

3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation

10.52 score 64 stars 2 packages 436 scripts 577 downloads

nat.nblast - NeuroAnatomy Toolbox ('nat') Extension for Assessing Neuron Similarity and Clustering

Extends package 'nat' (NeuroAnatomy Toolbox) by providing a collection of NBLAST-related functions for neuronal morphology comparison (Costa et al. (2016) <doi: 10.1016/j.neuron.2016.06.012>).

Last updated 3 months ago

morphological-analysisnblastneuroanatomyneuroanatomy-toolboxneurons

6.36 score 16 stars 96 scripts 161 downloads

nat.utils - File System Utility Functions for 'NeuroAnatomy Toolbox'

Utility functions that may be of general interest but are specifically required by the 'NeuroAnatomy Toolbox' ('nat'). Includes functions to provide a basic make style system to update files based on timestamp information, file locking and 'touch' utility. Convenience functions for working with file paths include 'abs2rel', 'split_path' and 'common_path'. Finally there are utility functions for working with 'zip' and 'gzip' files including integrity tests.

Last updated 3 months ago

natneuroanatomy-toolbox

4.13 score 3 packages 15 scripts 322 downloads

nat.templatebrains - NeuroAnatomy Toolbox ('nat') Extension for Handling Template Brains

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

Last updated 1 years ago

bridging-registrationsimage-registrationnatverseneuroanatomyneuroanatomy-toolbox

4.05 score 3 stars 37 scripts 255 downloads

natmanager - Install the 'Natverse' Packages from Scratch

Provides streamlined installation for packages from the 'natverse', a suite of R packages for computational neuroanatomy built on top of the 'nat' 'NeuroAnatomy Toolbox' package. Installation of the complete 'natverse' suite requires a 'GitHub' user account and personal access token 'GITHUB_PAT'. 'natmanager' will help the end user set this up if necessary.

Last updated 4 months ago

3.00 score 2 stars 1 scripts 328 downloads

dracor - Decode Draco Format 3D Mesh Data

Decodes meshes and point cloud data encoded by the Draco mesh compression library from Google. Note that this is only designed for basic decoding and not intended as a full scale wrapping of the Draco library.

Last updated 2 years ago

3d-meshnatverse

2.70 score 3 scripts 225 downloads

natcpp - Fast C++ Primitives for the 'NeuroAnatomy Toolbox'

Fast functions implemented in C++ via 'Rcpp' to support the 'NeuroAnatomy Toolbox' ('nat') ecosystem. These functions provide large speed-ups for basic manipulation of neuronal skeletons over pure R functions found in the 'nat' package. The expectation is that end users will not use this package directly, but instead the 'nat' package will automatically use routines from this package when it is available to enable large performance gains.

Last updated 3 years ago

computational-neuroscienceneuroanatomy-toolbox

2.70 score 4 scripts 160 downloads