Computer technologies can produce 3D representations of interesting human tissue and organs that have been serial-sectioned, dyed or stained, imaged, and segmented for 3D visualization 3D reconstruction also has great potential in the fields of tissue engineering and 3Dprinting.
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.
Interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions. The rapid detection of any errors that may occur greatly increases the productivity of recording sessions at the electron microscope.
Represents an algorithm based on the theory of compressed-sensing and the assumption of non-negativity density of biological specimen. ICON assists users to refurbish validated missing information for low signal to noise ratio (SNR) biological electron tomography (ET) dataset. Also, this tool checks and measures fidelity of the information restoration.
Provides a Platform-independent Object-Oriented framework for all data manipulations in tomographic imaging. STIR can be used to study existing and/or new reconstruction algorithms for a wide variety of cylindrical scanners. It enables the research community to study the performance of several algorithms on Single Photon Emission Computed Tomography (SPECT) data, and potentially implement new algorithms by expanding the existing framework. The tool offers the prospect to compare different Positron Emission Tomography (PET) scanners using identical correction and reconstruction software.
Improves fiducial marker tracking. gmm-marker-tracking is based on a Gaussian mixture model. It permits automatic tracking for datasets with a massive number of fiducial markers. This tool can represent a point set, and can provide a point set registration solution from the view of probability distribution. It may stuck in datasets with extremely irregular fiducial marker distributions.
Automates the alignment of dual-axis tilt series. AuTom-dualx is a toolkit intending to supply a general framework able to perform a simultaneous alignment and reconstruction for dual-axis electron tomography. This approach is composed of three main steps which first include the identification and the tracking of fiducial markers followed by the merging of two tilt series and, lastly, their optimization.
Provides solutions to users for viewing, modeling, and analyzing 3-D image data for structural biology. IMOD is designed for observing data from tomographic, serial section, and optical section reconstructions. Moreover, this program is also able to measure areas, volumes, and contour lengths, and to count objects of any model class.
Offers a platform for subtomograms analysis. TomoMiner is an open source software which consists of a set of methods for (i) large-scale subtomogram ranking (ii) template matching, (iii) averaging, and (iv) aligning. This application is able to handle more than 100 000 subtograms in a row. It aims to complement other existing approaches for analysis and exists as a standalone application or as a cloud-based implementation, called TomoMinerCloud, using Amazon AWS.
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.
Elaborates data acquisition schemes with autotuning functions and sophisticates image analysis routines. TOM Toolbox integrates established algorithms and concepts tailored to the special needs of low dose electron tomography (ET). It provides three-dimensional images not only of periodic or repetitive objects, but also of structures with unique topologies. The software represents a way of working with the electron microscope and can serve as the basis for high-throughput applications.
Aligns tomographic tilt series obtained from electron microscopes. RAPTOR is intended to automatically obtain a full-precision alignment comparable to the one obtained with extended manual intervention. Fiducial particles are needed in the image for the alignment. RAPTOR has been tested in many different datasets (cryo-EM, plastic, thick sections) and has given good results. RAPTOR has been incorporated into IMOD.
Provides solution for assembling situation-specific advanced tomographic reconstruction algorithms. Ettention is a set of modular building-blocks for tomographic reconstruction algorithms. It features: (1) a modular, object-oriented software design; (2) optimized access to high-performance computing (HPC) platforms such as graphic processing units (GPU); and (3) accessibility to microscopy end-users via integration in the IMOD package and eTomo user interface.
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.
Serves for microtubule-kinesin motor domain complexes. PEET is a program that can align particles in 3-D subvolumes extracted from tomograms. This tool seeks the optimal alignment of each particle against a reference volume through several iterations. The program utilizes the parallel processing framework within IMOD software, and the lengthy computations can be distributed to multiple cores on one computer, to a set of linked workstations, or to a cluster.
Serves for marker free alignment and 3D reconstruction. Protomo is based on cross-correlation methods and projection matching. It includes the refinement of geometric parameters of the tilt series. This software is dedicated to thin sections of insect flight muscle and paracrystalline protein arrays and can be applied to various specimens in cryo-electron tomography.
Serves three-dimensional reconstruction in transmission electron microscopy. TomoJ is a program allowing the automatic and semi-automatic alignment, that encompasses all algorithmic steps needed for tomographic reconstruction. One of the specificity of this tool is that it can perform 3D reconstruction using the ART and SIRT. Moreover, it has been written as a plug-in for ImageJ.
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 calculating regularized solutions to discretization of inverse problems. AIR Tools aims to provide easy-to-use implementations of the most important algebraic iterative reconstruction (AIR) methods. Each method is equipped with several stopping rules as well as heuristics for choosing the relaxation parameter. It is written for numerical analysts and application specialists who want to experiment with the iterative methods and their convergence properties.
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.
Assists in focusing microscopic images of 3D objects and organisms. Extended Depth of Field is based on different wavelet algorithms. This ImageJ plugin offers users two interfaces: a simplified mode and an expert mode with a complete set of parameters. It benefits from a RGB to grayscale conversion method that assures contrast and intensity in order to process color data.