Supplies an assortment of methods for real-space fitting of atomic models. EMFit is a standalone software composed of two main functions: (i) it can scale a map to another map by performing both vertical and horizontal scaling and; (ii) it is able to adjust set of atoms depicting a rigid molecule into an electron density map. Additionally, the application handles clashes between symmetry related positions.
It is an organized collection of software modules for image data handling, pre-processing, segmentation, inspection and editing, post-processing, and secondary analysis. These modules can be scripted to accomplish a variety of automated image analysis tasks.
Fits atomic models into Electron Microscopy (EM) reconstructions. UROX provide a graphical tool with real-time interactive fitting between the EM map and model-derived electron density. Regions of the map can be hidden from the display to simplify the visualization while effectively using the whole EM map or a part of it in the calculations. This software combines advantages of real-space visualization and reciprocal-space fast computation.
Allows users to image and rebuild biological samples. Mr. T is a module dedicated to tomography that aims to facilitate the acquisition of low-dose tilt series. It is able to perform offers specimen tracking by cross-correlation or by pre-calibration as well as control the electron microscope and detector. The application exploits features from the EMAN software and JAMES software libraries.
A broadly applicable algorithm and a comprehensive open-source software implementation for automated tracing of neuronal structures in 3-D microscopy images. Open Snake Tracing System has been integrated to the Farsight toolkit. The core 3-D neuron tracing algorithm is based on three-dimensional (3-D) open-curve active Contour (Snake). It is initiated from a set of automatically detected seed points. A suite of pre-processing algorithms enable the system to accommodate diverse neuronal image datasets by reducing them to a common image format. These algorithms form the basis for a comprehensive, scalable, and efficient software system developed for confocal or brightfield images. It provides multiple automated tracing modes. The user can optionally interact with the tracing system using multiple view visualization, and exercise full control to ensure a high quality reconstruction.