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2dSpAn
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.
SparseTracer
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.
SmartTracing
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.
FiloDetect
Obsolete
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.
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