Supplies method for automated detection of synapses from conventionally en-bloc stained 3D electron microscopy (EM) image stacks. SynEM aims to provide automated connectomes from large-scale EM data. It performs precision and recall for single-synapse detection and for binary neuron-to-neuron connectomes without any human interaction, essentially removing the synapse annotation challenge for large-scale mammalian connectomes.
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 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.
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