RANN - Fast Nearest Neighbour Search (Wraps ANN Library) Using L2 Metric
Finds the k nearest neighbours for every point in a given dataset in O(N log N) time using Arya and Mount's ANN library (v1.1.3). There is support for approximate as well as exact searches, fixed radius searches and 'bd' as well as 'kd' trees. The distance is computed using the L2 (Euclidean) metric. Please see package 'RANN.L1' for the same functionality using the L1 (Manhattan, taxicab) metric.
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ann-librarynearest-neighborsnearest-neighbourscpp
12.75 score 63 stars 261 dependents 1.8k scripts 63k downloads
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
11.00 score 77 stars 3 dependents 579 scripts 475 downloadsnabor - Wraps 'libnabo', a Fast K Nearest Neighbour Library for Low Dimensions
An R wrapper for 'libnabo', an exact or approximate k nearest neighbour library which is optimised for low dimensional spaces (e.g. 3D). 'libnabo' has speed and space advantages over the 'ANN' library wrapped by package 'RANN'. 'nabor' includes a knn function that is designed as a drop-in replacement for 'RANN' function nn2. In addition, objects which include the k-d tree search structure can be returned to speed up repeated queries of the same set of target points.
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libnabonearest-neighborscpp
8.74 score 21 stars 45 dependents 138 scripts 14k downloadsreadbitmap - Simple Unified Interface to Read Bitmap Images (BMP,JPEG,PNG,TIFF)
Identifies and reads Windows BMP, JPEG, PNG, and TIFF format bitmap images. Identification defaults to the use of the magic number embedded in the file rather than the file extension. Reading of JPEG and PNG image depends on libjpg and libpng libraries. See file INSTALL for details if necessary.
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bmpjpegpngtiff
8.07 score 4 stars 56 dependents 92 scripts 6.3k 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
7.32 score 17 stars 138 scripts 303 downloadsbmp - Read Windows Bitmap (BMP) Images
Reads Windows BMP format images. Currently limited to 8 bit greyscale images and 24,32 bit (A)RGB images. Pure R implementation without external dependencies.
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7.02 score 2 stars 60 dependents 57 scripts 5.1k downloadscolorRamps - Builds Color Tables
Builds gradient color maps.
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6.82 score 1 stars 48 dependents 1.8k scripts 3.7k 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
4.84 score 3 stars 58 scripts 554 downloadsreadobj - Fast Reader for 'Wavefront' OBJ 3D Scene Files
Wraps 'tiny_obj_loader' C++ library for reading the 'Wavefront' OBJ 3D file format including both mesh objects and materials files. The resultant R objects are either structured to match the 'tiny_obj_loader' internal data representation or in a form directly compatible with the 'rgl' package.
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3d-modelsrgltinyobjloaderwavefront-objcpp
4.83 score 8 stars 1 dependents 28 scripts 342 downloadsdendroextras - Extra Functions to Cut, Label and Colour Dendrogram Clusters
Provides extra functions to manipulate dendrograms that build on the base functions provided by the 'stats' package. The main functionality it is designed to add is the ability to colour all the edges in an object of class 'dendrogram' according to cluster membership i.e. each subtree is coloured, not just the terminal leaves. In addition it provides some utility functions to cut 'dendrogram' and 'hclust' objects and to set/get labels.
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4.64 score 3 dependents 98 scripts 584 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 337 downloadsIgorR - Read Binary Files Saved by 'Igor Pro' (Including 'Neuromatic' Data)
Provides function to read data from the 'Igor Pro' data analysis program by 'Wavemetrics'. The data formats supported are 'Igor' packed experiment format ('pxp') and 'Igor' binary wave ('ibw'). See: <https://www.wavemetrics.com/> for details. Also includes functions to load special 'pxp' files produced by the 'Igor Pro' 'Neuromatic' and 'Nclamp' packages for recording and analysing neuronal data. See <https://github.com/SilverLabUCL/NeuroMatic> for details.
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electrophysiologyigorneuromaticpro
3.85 score 7 stars 7 scripts 188 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 269 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
3.18 score 6 scripts 301 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 332 downloads