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Neuron tracing | Bioimaging software tools

The study of the structure and function of neuronal cells and networks is of crucial importance in the endeavor to understand how the brain works. A key component in this process is the extraction of neuronal morphology from microscopic imaging…
NeuroGPS-Tree
Desktop

NeuroGPS-Tree NeuronGlobalPositionSystem-Tree

Reconstructs neuronal population from image stacks. NeuroGPS-Tree is built on…

Reconstructs neuronal population from image stacks. NeuroGPS-Tree is built on NeuroGPS software. In NeuroGPS-Tree reconstruction, individual neuronal trees can be identified and quantified.…

nat.nblast
Desktop

nat.nblast

Allows to implement NBLAST neuron similarity algorithm. Nat.nblast is an…

Allows to implement NBLAST neuron similarity algorithm. Nat.nblast is an extension of the “nat” software, and supplies a collection of NBLAST-related functions. It executes search of databases…

SmartScope2
Desktop

SmartScope2

Automates neuron reconstruction machine integrating online image analysis with…

Automates neuron reconstruction machine integrating online image analysis with automated multiphoton imaging. SmartScope2 takes advantage of a neuron’s sparse morphology to improve imaging speed…

Rivuletpy
Desktop

Rivuletpy

Tracks iteratively the potential neuronal termini to the soma centre. Rivuletpy…

Tracks iteratively the potential neuronal termini to the soma centre. Rivuletpy is a Python toolkit for automatically reconstructing single neuron models from 3D microscopic image stacks. This…

NeRVEclustering
Desktop

NeRVEclustering Neuron Registration Vector Encoding

Allows to track populations of neurons with single neuron resolution in the…

Allows to track populations of neurons with single neuron resolution in the brain of a freely moving C. elegans undergoing large motion and deformation. NeRVEclustering uses non-rigid point-set…

hgpush
Desktop

hgpush

A statistical method for tracing the branch centerlines of neurons based on…

A statistical method for tracing the branch centerlines of neurons based on Bayesian multi-object tracking using probability hypothesis density (PHD) filtering. hgpush is able to simultaneously trace…

2dSpAn
Desktop

2dSpAn

A method for 2-d segmentation, classification and analysis of…

A method for 2-d segmentation, classification and analysis of structural/plastic changes of hippocampal dendritic spines. A user interactive segmentation method with convolution kernels is designed…

AnaMorph
Desktop

AnaMorph

Automatically generates water-tight surface meshes from one-dimensional…

Automatically generates water-tight surface meshes from one-dimensional point-diameter files. AnaMorph is a framework based on non-linear piecewise analytical modeling and using the existing…

Neuron Crawler
Desktop

Neuron Crawler

An automatic tracing algorithm. Neuron Crawler works by first tracing a region…

An automatic tracing algorithm. Neuron Crawler works by first tracing a region of interest (e.g., around the soma), and then iteratively tracing in adjacent image tiles to grow the neuron structure…

SmartTracing
Desktop

SmartTracing

An automatic tracing framework for neuron reconstruction that does not require…

An automatic tracing framework for neuron reconstruction that does not require substantial human intervention. SmartTracing algorithm has been implemented as a plugin of Vaa3D, which is the common…

UltraTracer
Desktop

UltraTracer

Designed to extend any base neuron-tracing algorithm to be able to trace…

Designed to extend any base neuron-tracing algorithm to be able to trace virtually unlimited data volumes. UltraTracer was applied to neuron-tracing algorithms with different design principles and…

BIDS Apps
Desktop

BIDS Apps Brain Imaging Data Structure Applications

A framework for creating, testing, versioning and archiving portable…

A framework for creating, testing, versioning and archiving portable applications for analyzing neuroimaging data organized and described in compliance with the Brain Imaging Data Structure (BIDS). A…

neuTube
Desktop

neuTube

A software tool for reconstructing neurons from fluorescence microscope images.…

A software tool for reconstructing neurons from fluorescence microscope images. The main function of neuTube is to generate a neuron structure from a 3D image with user interaction, which mainly…

SparseTracer
Desktop

SparseTracer

A pipeline for the reconstruction of discontinuous neuronal morphology in noisy…

A pipeline for the reconstruction of discontinuous neuronal morphology in noisy images. SparseTracer is based on two methods. One is the region-to-region connection (RRC) method for detecting the…

APP
Desktop

APP All-Path-Pruning

A software for 3D neuron tracing. APP2 prunes an initial reconstruction tree of…

A software for 3D neuron tracing. APP2 prunes an initial reconstruction tree of a neuron’s morphology using a long-segment-first hierarchical procedure instead of the original termini-first-search…

LM
Desktop

LM L-Measure

A freely available software tool for the quantitative characterization of…

A freely available software tool for the quantitative characterization of neuronal morphology. L-Measure computes a large number of neuroanatomical parameters from 3D digital reconstruction files…

Rayburst…
Algorithm

Rayburst sampling

An algorithm for automated three-dimensional shape analysis from laser scanning…

An algorithm for automated three-dimensional shape analysis from laser scanning microscopy images. The Rayburst algorithm provides a primitive for the development of higher level algorithms that…

flNeuronTool
Desktop

flNeuronTool

Allows users to reconstruct and proofread neuronal morphologies in light…

Allows users to reconstruct and proofread neuronal morphologies in light microscopy images. The system incorporates automatic tracing and manual editing of neuron reconstruction into a cooperative 3D…

Suite2p
Desktop

Suite2p

Provides a complete set of tools for two photon processing, with good…

Provides a complete set of tools for two photon processing, with good performance and fast run times. The Suite2p pipeline is modular, allowing the main processing steps to be used independently:…

zebrafishimage
Desktop

zebrafishimage

Extracts of quantitative information from green fluorescent protein (eGFP) and…

Extracts of quantitative information from green fluorescent protein (eGFP) and red fluorescent protein (RFP) labeled spinal cord neurons in double-transgenic zebrafish embryos. zebrafishimage…

WIS-NeuroMath
Desktop

WIS-NeuroMath

A software tool for automated analysis and quantification of fluorescent…

A software tool for automated analysis and quantification of fluorescent microscopy images of nerve cells, in both in vivo and in vitro preparations. Diverse image types can be analyzed without any…

NeuronStudio
Desktop

NeuronStudio

Allows reconstruction of neuronal structures from confocal and multi-photon…

Allows reconstruction of neuronal structures from confocal and multi-photon images. NeuronStudio provides tools for manual, semi-manual, and automatic tracing of the dendritic arbor as well as manual…

NAT
Desktop

NAT NeuroAnatomy Toolbox

Allows to realize analysis and visualisation of 3D biological image data, and…

Allows to realize analysis and visualisation of 3D biological image data, and more particularly traced neurons. NAT accepts 3D images in NRRD and 'Amira' AmiraMesh formats. The data can be…

Aivia
Desktop

Aivia

Combines state-of-the-art automated neuron tracing and machine learning-enabled…

Combines state-of-the-art automated neuron tracing and machine learning-enabled neuron classification tools. Aivia provides methods for analyzing time-lapse images. It covers a wide range of…

BIDS Validator
Web
Desktop

BIDS Validator Brain Imaging Data Structure Validator

Validates Brain Imaging Data Structure. BIDS Validator has one primary method…

Validates Brain Imaging Data Structure. BIDS Validator has one primary method that takes a directory as either a path to the directory (node) or the object given by selecting a directory with a file…

AxonTracker-3D
Desktop

AxonTracker-3D

An interactive 3D axon tracking and labeling tool to obtain quantitative…

An interactive 3D axon tracking and labeling tool to obtain quantitative information by reconstruction of the axonal structures in the entire innervation field. AxonTracker-3D has been developed to…

Simple Neurite…
Desktop

Simple Neurite Tracer

An application for semi-automated tracing of neurons to quickly annotate noisy…

An application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies. Simple Neurite Tracer is designed to allow easy semi-automatic…

GENESIS
Desktop

GENESIS GEneral NEural SImulation System

A general purpose simulation platform that was developed to support the…

A general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons,…

Open Snake…
Desktop

Open Snake Tracing System

A broadly applicable algorithm and a comprehensive open-source software…

A broadly applicable algorithm and a comprehensive open-source software implementation for automated tracing of neuronal structures in 3-D microscopy images. Open Snake Tracing System has been…

NETMORPH
Desktop

NETMORPH

A simulation framework for the developmental generation of 3D large-scale…

A simulation framework for the developmental generation of 3D large-scale neuronal networks with realistic neuron morphologies. In NETMORPH, neuronal morphogenesis is simulated from the perspective…

NeuGen
Desktop

NeuGen Neuron Network Generator

It is made for generation of dendritic and axonal morphology of realistic…

It is made for generation of dendritic and axonal morphology of realistic neurons and networks in 3D. The generated neurons can be exported into a 3D graphic format for visualization and into…

DF-Tracing
Algorithm

DF-Tracing Distance-Field Tracing

An automatic neuron tracing method. DF-Tracing can automatically trace…

An automatic neuron tracing method. DF-Tracing can automatically trace complicated neuron structures set in noise-contaminated microscopic images. This method first extracts the neurite signal…

L-Neuron
Desktop

L-Neuron

A software package for the generation and study of anatomically accurate…

A software package for the generation and study of anatomically accurate neuronal analogs. L-Neuron is based on sets of recursive rules that parsimoniously describe dendritic geometry and topology by…

NeuriteQuant
Desktop

NeuriteQuant

A freely available open-source tool for the automated analysis and effective…

A freely available open-source tool for the automated analysis and effective review of large-scale high-content screens. NeuriteQuant enables fully automated morphological analysis of large-scale…

FiloDetect
Desktop

FiloDetect

An automated tool for detecting, counting and measuring the length of filopodia…

An automated tool for detecting, counting and measuring the length of filopodia in fluorescence microscopy images. The method first segments the cell from the background, using a modified triangle…

NeuroM
Desktop

NeuroM

Allows users to analyze and process neuron morphologies. NeuroM is a…

Allows users to analyze and process neuron morphologies. NeuroM is a Python-based toolkit that authorizes users to extract morphometrics with more than ten different specific properties including…

morphology_anal…
Desktop

morphology_analysis

Analyzes large-scale neuron reconstructions or morphologies.

Analyzes large-scale neuron reconstructions or morphologies.

Neuronize
Desktop

Neuronize

Builds 3D neural meshes. Neuronize is a set of methods designed taking the…

Builds 3D neural meshes. Neuronize is a set of methods designed taking the morphological information extracted through computer-aided tracing applications as the starting point. The software…

NeuronGPS
Desktop

NeuronGPS NeuronGlobalPositionSystem

Automatically and accurately locates neurons, which is helpful for neuronal…

Automatically and accurately locates neurons, which is helpful for neuronal dendritic tracing. NeuroGPS locates the cell body by computing the radius of each soma, and finding the most preferred…

Neuron…
Desktop

Neuron reconstruction

A pipeline for reconstructing neuron anatomy structure from 3-D microscopy…

A pipeline for reconstructing neuron anatomy structure from 3-D microscopy image stacks. This pipeline is initialized with a set of seeds that were detected by our proposed Sliding Volume Filter…

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