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 data.
Allows users to visualize 3D/4D/5D image and to analyze system for bioimages and surface objects. Vaa3D consists of a container of modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics) and data management. Moreover, this platform can be used for developing 3D image analysis algorithms for high-throughput processing.
Assists in automating and multithreading Sholl for direct analysis of fluorescent images and traced morphologies. Sholl analysis is a plugin for the image analysis software ImageJ. It creates a serie of concentric circles around the soma of the neuron, and counts how many times the neuron intersects with the circumference of these circles. This software can be applied universally to gray-scale images of neurons of different shapes or sizes.
Allows 3D image data annotation in various 3D image analysis settings in connectomics and other fields. webKnossos is an in-browser annotation tool. The software accelerates human 3D data interaction for electron microscopic (EM)-based connectomics in browser by about 4- to 13-fold, which likely saturates human interaction speed with 3D EM data of nervous tissue using flight mode.
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 tested on challenging human and mouse neuron datasets that have hundreds of billions of voxels. Results indicate that UltraTracer is scalable, accurate, and about 3 to 6 times more efficient compared to other state-of-the-art approaches.
A quantification method capable of automatically quantifying neuronal morphologies such as soma number and size, neurite length, and neurite branching complexity (which is highly related to the numbers of attachment points and ending points). NeurphologyJ is implemented as a plugin to ImageJ, an open-source Java-based image processing and analysis platform.
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 for neurons, and permits to compare groups of neurons. A distance matrix for hierarchical clustering can be produced by this tool.
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 solve specific shape analysis problems. Examples are provided of applications to 3D neuronal morphometry: (i) estimation of diameters in tubular neuronal dendritic branching structures, and (ii) measurement of volumes and surface areas for dendritic spines and spatially complex histopathologic structures.
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 starting from and combining a set of core metrics.
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 and automatic detection and classification of dendritic spines. In addition, advanced 2D and 3D visualization techniques facilitate the verification of the reconstruction, as well as allowing accurate manual editing.
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 tracing of neurons or other tube-like structures (e.g. blood vessels) through 3D image stacks. The plugin has built-in tools for analysis and hardware accelerated 3D visualization of the results. Data can be imported and exported in SWC files for interaction with other software, or details of the traces can be exported as CSV files for analysis in spreadsheets or statistical software. The native file format is open and XML-based.
Allows to navigate, share and collaboratively annotate massive image data sets of biological specimens. CATMAID combines three main components: a centralized data server, decentralized image servers and the client-side user interface. The interface is applicable to any 2D or 3D multimodal biological image datasets, as shown in examples of stitched confocal 3D volumes. Additionally, the interface can be used to navigate, annotate and bookmark locations in any large image canvas.
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 process in APP. This method allows users to trace large images. APP2 was bench-tested on 700 3D microscopic images and it was found that APP2 can generate more satisfactory results in most cases than several previous methods. This software has been implemented as an open-source Vaa3D plugin.
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 facilitate the connectome function analysis in large-scale quantitative neurobiology studies. It can display the three orthogonal views of the current location of the centerline along with a visualization of the tracking results. The workflow consists of three steps: (i) re-slice the axon tubes along its orientation; (ii) extract 2D and 3D features from the slices and spheres rounding the center points; (iii) select samples to train AdaBoost classifier. Questions such as whether the spatial distribution of the axons are random in nature or follow a certain pattern can be answered with this tool.
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 to segment the spines from the dendrites. Formal morphological definitions are presented to describe key attributes related to the shape of segmented spines. Spines are automatically classified into one of four classes: Stubby, Filopodia, Mushroom and Spine-head Protrusions. 2dSpAn is a tool for fast and accurate annotation of dendritic spines from confocal microscopy images. However, the 2dSpAn method allows determining the morphology of spines from super-resolution microscopy and is not limited only to confocal images.
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 out multiple neuron structures in a probabilistic fashion so that the same neuron segments may be covered multiple times and are thus supported by more evidence. The main novelty is that it combines the problems of neuron segment detection and linking into one framework by performing simultaneous multi-object tracking. hgpush solves the computational problems of direct Bayesian multi-object tracking and allows convenient handling of bifurcations and terminations during the tracing process by modeling of spawned objects and observation clutter.
Offers a platform for handling dendritic structures. TREES Toolbox is a standalone software that allows users to create realistic synthetic branched structures and to automatically rebuild neuronal branching. The application provides methods to investigate and visualize both dendritic and axonal trees as well as their branching. The application is also able to compare multiple branching structures.
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 registration in order to match each segmented neuron in each volume with a set of reference volumes taken from throughout the recording. This tool primarily serves for tracking neurons in brains undergoing large deformations.
Calculates a set of characteristic morphological measures for a given three-dimensional spine reconstruction. 3DSpineMFE can be employed to estimate the spine shape. It splits the surface of the spine into regions according to a multi-resolutional Reeb graph to make the spine’s description. This tool projects the distances between the membership probabilities of the spines in a 6D space to 2D according to multidimensional scaling.
Defines dendritic spine geometry to gather dendritic spines using model-based clustering. 3DSpineMFE models simulated spines constructing their 3D representations. It uncovers six separate groups of human dendritic spines. This tool enables researchers to mimic realistic 3D virtual representations of spines that matched the morphological definitions of each cluster. It can serve to make theoretical estimations on the functional features of human pyramidal neurons.
Detects special cell type called astrocytes. FMC is an automated solution that pinpoints astrocytes on microscopy bright-field images. It can also be used to recognize other objects if the underlying deep convolutional neural network (DCNN) module is configured to identify other complex morphologies.