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.
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.
Denoises and pre-segments noisy electron microscopy tomograms. XMSF is a program that filters noise while preserving the structures of interest. The software can be used to process both 2D (images) and 3D (volumes) datasets. It has potential of application in electron tomography (ET). This program is available both as a stand-alone statically compiled executable and as part of the Xmipp image processing software package.
Serves for tomographic reconstruction that removes artefacts caused by contamination present in samples during imaging by electron microscopy. MaskTomRec is based on an iterative procedure involving reprojections of selected regions and 3D reconstructions. This approach is based on an iterative procedure involving reprojections of selected regions and 3D reconstructions, and can improve the resolution reached in cryo-tomograms.
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.
Improves results for Signal-to-Noise Ratios (SNR) lower than 0.1. TCCC allows to analyze macromolecules in thicker samples like whole cell or lower the defocus in thinner samples to push the first zero of the Contrast Transfer Function (CTF). TCCC uses statistics of the noise to automatically select only a small percentage of the Fourier coefficients to compute the cross-correlation. The thresholding has two main advantages in the cross-correlation score: first, reduces the influence of the noise; second, avoids the missing wedge normalization problem since we consider the same amount of coefficients for all possible pairs of subtomograms.
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.
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.
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.
Offers a collection of filters for 3D images supported by Java Native Interface. FastFilter3D performs several 3D filtering on 8-bits and 16-16-bits gray-levels stacks. This ImageJ plugin performs the following 3D filters: median, mean, minimum, maximum, maximum local and topchat.
Assists in processing energy filtering transmission electron microscope (EFTEM). EFTEMj is a plugin for the image processing software ImageJ that contains several modules for distinct features. Six modules allows, amongst others, the loading of msa-files, the measure of elemental maps from EFTEM images, the preservation of spatial information when recording Electron Energy Loss (EEL) spectra or the use of python scripts.
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