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.
Provides the essential tools for the analysis of subtomograms obtained by cryo electron tomography. PyTom covers a processing pipeline of tomogram reconstruction, localization of macromolecular complexes in tomograms, fine alignment of subtomograms extracted at these locations and their classification. PyTom is mostly written in Python making it fairly easy to add new functionality as well as to customize existing methods for specific purposes. The package is mainly developed in the Förster lab at the Max Planck Institute for Biochemistry, but developers are highly encouraged to contribute to PyTom on an open source basis.
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.
Provides a root system architecture characterization software. ARIA is based on a mathematically rigorous approach of converting root images into graphs. It automates phenotyping with the potential of adding additional features. This tool completes large phenotyping experiments required for many quantitative genetic studies. It is able to analyze 2D flat plane images and 3D images of roots.
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