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.

Last updated 7 months ago

ann-librarynearest-neighborsnearest-neighbourscpp

12.21 score 58 stars 190 dependents 1.3k scripts 38k 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).

Last updated 5 months ago

3dconnectomicsimage-analysisneuroanatomyneuroanatomy-toolboxneuronneuron-morphologyneurosciencevisualisation

10.24 score 66 stars 2 dependents 436 scripts 607 downloads

nabor - 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.

Last updated 5 years ago

libnabonearest-neighborscpp

8.21 score 22 stars 34 dependents 104 scripts 6.9k downloads

readbitmap - 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.

Last updated 7 years ago

bmpjpegpngtiff

8.01 score 4 stars 58 dependents 75 scripts 6.6k downloads

colorRamps - Builds Color Tables

Builds gradient color maps.

Last updated 1 years ago

6.82 score 1 stars 46 dependents 1.7k scripts 4.1k 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 6 months ago

morphological-analysisnblastneuroanatomyneuroanatomy-toolboxneurons

6.69 score 17 stars 96 scripts 226 downloads

bmp - 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.

Last updated 7 years ago

6.36 score 1 stars 62 dependents 39 scripts 6.4k downloads

readobj - 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.

Last updated 3 years ago

3d-modelsrgltinyobjloaderwavefront-objcpp

4.64 score 8 stars 1 dependents 18 scripts 367 downloads

dendroextras - 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.

Last updated 7 years ago

4.61 score 3 dependents 90 scripts 475 downloads

IgorR - 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.

Last updated 7 months ago

electrophysiologyigorneuromaticpro

4.32 score 7 stars 6 scripts 300 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 6 months ago

natneuroanatomy-toolbox

4.13 score 3 dependents 15 scripts 429 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 2 years ago

bridging-registrationsimage-registrationnatverseneuroanatomyneuroanatomy-toolbox

4.05 score 3 stars 37 scripts 239 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 8 months ago

3.00 score 2 stars 1 scripts 437 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-meshnatversecpp

2.70 score 3 scripts 304 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-toolboxcpp

2.70 score 4 scripts 150 downloads