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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.


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.


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.

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.

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.


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 preprocessing, enabling automated and accurate detection of neurites followed by their quantification in a number of application modules. A cell morphology module detects cell bodies and attached neurites, providing information on neurite length, number of branches, cell body area, and other parameters for each cell. A neurite length module provides a solution for images lacking cell bodies, such as tissue sections. Finally, a ganglion explant module quantifies outgrowth by identifying neurites at different distances from the ganglion. Quantification of a diverse series of preparations with WIS-NeuroMath provided data that were well matched with parallel analyses of the same preparations in established software packages such as MetaXpress or NeuronJ.


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 threshold method, and then extracts the filopodia using a series of morphological operations. FiloDetect provides accurate and objective quantification of filopodia in microscopy images, and will enable large scale comparative studies to assess the effects of different genetic and chemical perturbations on filopodia production in different cell types, including cancer cell lines.