Describes the reconstruction of biological molecules from the electron micrographs of single particles. SPIDER is an open source project that manages computation using the image-processing software and can also using a graphical user interface (GUI), termed the SPIDER Reconstruction Engine. These two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines.
Processes and analyses electron microscopy (EM) images. Appion is integrated with Leginon data acquisition but can also be used stand-alone after uploading images (either digital or scanned micrographs) or particle stacks using a set of provided tools. Appion consists of a web based user interface linked to a set of python scripts that control several underlying integrated processing packages. All data input and output within Appion is managed using tightly integrated SQL databases. The goal is to have all control of the processing pipeline managed from a web based user interface and all output from the processing presented using web based viewing tools.
Serves for effective segmentation of multidimensional datasets. MIB can recognize several number of imaging formats and offers a variety of image processing tools. It also simplifies utilization and quantification of acquired data. It permits users to segment large datasets, to realize 3D visualization, and to quantify images and models. Its parameters enable users to insert plugin s to customize the program for specific needs.
Aims to study synaptic vesicles in electron tomograms. FIJI Macro 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Furthermore, it shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation.
Allows users to detect different membranes. TomoSegMenTV is a procedure for membrane segmentation based on tensor voting and is able to fill gaps present along the membranes. This program consists of the following steps: (1) filtering and scale-space of the input tomogram; (2) tensor voting on surface saliency; (3) local surface detection and characterization; (4) tensor voting for bridging gaps; (5) local membrane detector; and (6) thresholding and global analysis.
Segments low signal-to-noise ratio (SNR) data typical of 3D reconstructed volumes. RAZA is a detection algorithm that integrates a Laplacian of Gaussian (LoG) kernel, with arbitrary z-crossings and structural finger printing algorithms. It can detect edges in the tomographic volume, the edges are defined as regions exhibiting a “significant change” in voxel intensity compared to their surroundings. It defines each continuous contour within a tomographic volume as a discrete geometric object, as opposed to conducting simple pixel based edge delineation.
Allows users to segment membranes in tomograms. TOMOSEGMEM is an algorithm for membrane segmentation that relies on a simple local membrane model and the local differential structure to determine points whose neighborhood resembles plane-like features. It is composed of several sequential stages, consisting of: (1) isolation of information at a suitable scale and find potential membrane-like features according to local detectors and (2) analysis and integration of the structural information at a global scale.
Allows users to analyze and visualize electron microscope (EM) tomography data. EM3D is a program that contains a graphical user interface (GUI), and that can combine dual axis data sets, i.e two data sets taken orthogonal to one another. It provides a set of analysis tools to quantify structural information from the models, including their moments, proximity relationships, and spatial reliability.
Assists in exploration of possible watershed segmentation. Interactive-H-Watershed is a plugin for the image analysis software ImageJ. It provides an interactive way to explore local minima (maxima) on the fly. This module is based on Watershed, a common tool to segment objects in an 2D and 3D images. The method permits to gradually flood the valleys starting from their lowest point.
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.
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