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.
Allows image processing of electron micrographs, interpretation of reconstructions, molecular modeling, and general image processing. The Bsoft code is modularized to allow for rapid testing and deployment of new processing algorithms, while also providing sufficient infrastructure to deal with many file formats and parametric data. The design is deliberately open to allow interchange of information with other image and molecular processing software through a standard parameter file and its support of multiple image and molecular formats. The graphical user interface is the program bshow, which is used for many interactive purposes such as fitting the contrast transfer function or picking particles. Bsoft also offers various tools to manipulate atomic structures and to refine the fit of a known molecular structure to a density in a reconstruction.
A simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode.
Allows users to segment cryo-electron microscopy (cryo-EM) density maps. Segger is a module, based on watershed and scale space filtering, that can be run through the Chimera software. The application employs segmented regions to enable rigid-body docking of known structures within density maps. It also interprets the quality and reliability of the docking results by calculating atom inclusion, density occupancy, and clashes with symmetry-related copies.
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.
Performs electron microscopy (EM) based segmentation of images in nifti or analyse format. NiftySeg contains a package of label fusion algorithms (MV, STAPLE, SBA) with different types of ranking strategies.
Splits microscopy data dealing with axon and myelin. AxonDeepSeg provides a standalone software able to create models for new imaging procedures as well as to perform semantic segmentation of histological images. The application includes two models for both scanning electron microscopy (SEM) and transmission electron microscopy (TEM) samples segmentation. It can be applied to the study of the distribution and size of myelinated fibers in samples.