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.
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.
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.
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.
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.
Implements a multithreaded-vectorized approach to tomographic reconstruction. TOMO3D allows computation of full resolution tomograms at high speed on standard computers. The software is compatible with standard packages in the field, allowing integration in the electron tomography workflow. It is available for predominant processing platforms and can also be built for other platforms on request to authors.
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.