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natverse
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).
Maintained by Gregory Jefferis. Last updated 5 months ago.
3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
20.9 match 67 stars 9.94 score 436 scripts 2 dependentsnatverse
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>).
Maintained by Gregory Jefferis. Last updated 7 months ago.
morphological-analysisnblastneuroanatomyneuroanatomy-toolboxneurons
20.8 match 17 stars 6.69 score 96 scriptsnatverse
nat.templatebrains:NeuroAnatomy Toolbox ('nat') Extension for Handling Template Brains
Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.
Maintained by Gregory Jefferis. Last updated 2 years ago.
bridging-registrationsimage-registrationnatverseneuroanatomyneuroanatomy-toolbox
20.9 match 3 stars 4.05 score 37 scriptsnatverse
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.
Maintained by Gregory Jefferis. Last updated 7 months ago.
10.9 match 4.13 score 15 scripts 3 dependentsnatverse
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.
Maintained by Gregory Jefferis. Last updated 3 years ago.
computational-neuroscienceneuroanatomy-toolboxcpp
11.0 match 2.70 score 4 scriptsnatverse
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.
Maintained by Gregory Jefferis. Last updated 8 months ago.
0.8 match 2 stars 3.00 score 1 scripts