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.
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.
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.
Collects single-axis tilt series on electron transmission microscopes. UCSF Tomography is a software that was implemented based upon an approach in which the compustage tilting is modeled as geometric rotation. The spatial movement of the sample as a result of stage tilting can be predicted based upon previously collected tomographic images. It has been proven to be very robust in collecting cryo tilt series on thin and thick samples at various magnifications up to 60,000x.
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.
Filters noise in tomograms. TOMOAND is a 3D anisotropic nonlinear diffusion method that simultaneously combines the EED (Edge-Enhancing Diffusion) and CED (Coherence-Enhancing Diffusion) diffusion modes. The software analyzes each voxel in the volume to define if it is part of (1) an isotropic feature or noise or (2) a plane-like or line-like feature.
Serves for noise reduction with feature-preserving capabilities based upon geometric flow. TOMOBFLOW is a program containing power of diffusion-based noise filtering approaches. It can filter 3D volumes, individual 2D images, or stacks of 2D images. It applies an isotropic nonlinear filtering method based on the Beltrami flow, which tunes the strength of the smoothing according to a local edge indicator.