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Rayburst sampling
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.
Simple Neurite Tracer
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.
CATMAID / Collaborative Annotation Toolkit for Massive Amounts of Image Data
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.
APP / All-Path-Pruning
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.
Open Snake Tracing System
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 integrated to the Farsight toolkit. The core 3-D neuron tracing algorithm is based on three-dimensional (3-D) open-curve active Contour (Snake). It is initiated from a set of automatically detected seed points. A suite of pre-processing algorithms enable the system to accommodate diverse neuronal image datasets by reducing them to a common image format. These algorithms form the basis for a comprehensive, scalable, and efficient software system developed for confocal or brightfield images. It provides multiple automated tracing modes. The user can optionally interact with the tracing system using multiple view visualization, and exercise full control to ensure a high quality reconstruction.
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 generates 3D models for neuronal cells that approximate the cell membrane at different resolution levels, allowing balance to be reached between the complexity and the quality of the final model. The software is conceived to overcome the problems caused by the unrealistic somata and low quality unconnected 3D mesh.
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 reconstruction data as the “spine” for the computed canal-surfaces of dendritic and axonal arbors of neurons. The software can be used to simulate the electrical and biochemical behavior of the underlying cell. It can also perform quality control of the semi-automatically reconstructed cells coming from anatomical reconstructions.
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 initial part of a neurite, which can effectively gather local cues, i.e., avoid the whole image analysis, and thus boosts the efficacy of computation. The other is constrained principal curves method for completing the neurite reconstruction, which uses the past reconstruction information of a neurite for current reconstruction and thus can be suitable for tracing discontinuous neurites. SparseTracer is able to deal with the large-scale image dataset.
Provides quantitative morphological analysis of static 2D images of fluorescent cultured neurons. NeuronMetrics is a modular semi-automated software, written as plug-ins for ImageJ, that can be used to analyze sets of images of individual fluorescently labeled cultured neurons with complex arbors, including in the presence of moderate background noise. The software can process images with non-uniform fluorescent signal by using empirically determined image-processing parameters that allow good skeletonization.
An easy to use software application that will greatly speed and standardize quantification of neuron organization. IPLaminator rapidly analyzes neurite stratification patterns in the retina and other neural tissues. A range of user options allows researchers to bin inner plexiform layer (IPL) stratification based on fixed points, such as the neurites of cholinergic amacrine cells, or to define a number of bins into which the IPL will be divided. Options to analyze tissues such as cortex were also added. Statistical analysis of the output then allows a quantitative value to be assigned to differences in laminar patterning observed in different models, genotypes or across developmental time.
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: registration, cell detection, spike deconvolution and manual GUI. This allowed to routinely record and detect approximately 10,000 cells simultaneously from the visual cortex of awake mice using standard two-photon resonant-scanning microscopes. The software is publicly available with a graphical user interface (GUI) that allows rapid manual curation of the results.
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 platform to implement algorithms for the BigNeuron project bench-testing. SmartTracing does not require human input of training exemplars and can self-adapt to different types of neuroimage data. Additionally, the method can be applied to improve the performance of other existing tracing methods.
Neuron Crawler
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 in 3D to its termination point within the image. It makes it possible to reconstruct very large 3D images. Experimental results show that Neuron Crawler can achieve reconstruction accuracy that is comparable to several state-of-the art algorithms, but with much less computational cost. Neuron Crawler is implemented as a plugin of Vaa3D.
Amira 3D Software for Life Sciences
Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.
NeuroGPS-Tree / NeuronGlobalPositionSystem-Tree
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. NeuroGPS-Tree reconstructs neuronal populations by partially mimicking the strategy used by experienced annotators and progressively approaches an accurate reconstruction by repetitively using statistical information about neuronal morphology at multiple scales. These features make NeuroGPS-Tree an effective tool for analyzing data sets in which the neurite density is too complex for previously established methods. NeuroGPS-Tree is also suitable for the analysis of large-scale data sets, and it may be useful for mapping neuronal circuits.
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