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).
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3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation
10.88 score 77 stars 3 dependents 549 scripts 458 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>).
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morphological-analysisnblastneuroanatomyneuroanatomy-toolboxneurons
7.18 score 17 stars 100 scripts 161 downloadsnat.templatebrains - NeuroAnatomy Toolbox ('nat') Extension for Handling Template Brains
Extends package 'nat' (NeuroAnatomy Toolbox) by providing objects and functions for handling template brains.
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bridging-registrationsimage-registrationnatverseneuroanatomyneuroanatomy-toolbox
4.81 score 3 stars 54 scripts 543 downloadsnat.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.
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natneuroanatomy-toolbox
4.26 score 4 dependents 15 scripts 374 downloadsnatmanager - 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.
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3.78 score 4 stars 1 scripts 257 downloadsnatcpp - 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.
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computational-neuroscienceneuroanatomy-toolboxcpp
3.00 score 5 scripts 168 downloadsdracor - 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.
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3d-meshnatversecpp
2.70 score 3 scripts 251 downloads