Serial block face imaging three-dimensional reconstruction software tools | Cryo-electron microscopy image analysis
Commercial automated systems are now available, such as the Gatan 3View system and the FEI VolumeScope system, where automated sectioning and capture systems are located in a variable pressure, field emission gun, environmental scanning electron microscope (FEG-ESEM). Sequential ultramicrotomy and imaging produce a stack of aligned images that can be viewed in sequence, or further processed using 3D reconstruction and analysis software. Automation has allowed acquisition workflows delivering very large 3D datasets at electron microscope resolution, for example to reconstruct the connectivity of neuronal circuits in brain mapping.
Uses an approach based on prediction of specimen position during the tilt series from the position at previous tilts. SerialEM is a program that can acquire a variety of data from electron microscopes: tilt series for electron tomography, large image areas for 3-D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods. In addition to automating data acquisition, the program provides an integrated user interface for image acquisition, display, and storage.
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.
Analyzes, processes and visualizes multi-dimensional microscopy images. BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes.
A three-dimensional (3D) reconstruction and modeling software. Free-D allows to generate, process and analyze 3D point and surface models from stacks of 2D images. It is an integrated software tool, offering in a single graphical user interface all the functionalities required for 3D modeling.
Estimates the positions and spacing between sections (or at local points) of three dimensional image data. Z-Spacing is an image-based method for the correction of continuous and discontinuous non-planar axial distortions in serial section microscopy. It may be applied to any imaging modality that acquires 3-dimensional data as a stack of 2-dimensional sections. It also provides plugins for both Fiji and TrakEM2.
Provides assistance for elastic volume reconstruction via series of ultra-thin microscopy sections. Elastic Alignment and Montage works for the ImageJ software through the TrakEM2 toolkit. This elastic alignment method is appropriate for groups of overlapping 2D-images. It enables the montage of mosaics from overlapping tiles and the alignment of deformed section series from serially sectioned volumes.
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.