Allows automated collection of images from a transmission electron microscope. Leginon proposes a flexible architecture to allow for the development of customized data collection protocols. The system has been used to acquire data for approximately 150 experiments and has demonstrated the capacity for high throughput data acquisition by acquiring images of more than 100 000 particles in a single session at the microscope. Leginon system includes python-side programs, a MySQL database and server, and php-based image and data viewers on a web server.
Provides users with all aspects of cryo-electron microscopy (cryo-EM) structure determination, from micrograph motion correction to atomic model refinement. Cryo-EM Cloud Tools combines the full RELION pipeline (and associated software) with atomic model building and refinement with Rosetta and with Amazon web services (AWS). The software provides “burstable” processing power, ensuring that data processing does not become rate-limiting ahead of grant and manuscript deadlines. It can have an impact on cryo-EM facilities with a large user base.
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.
Facilitates efficient acquisition, on-the-fly motion correction, and CTF analysis of dose fractionated image stacks. UCSFImage is a computer-assisted system for semi-automated electron cryomicroscopy (cryoEM) image acquisition that implements an asynchronous data acquisition scheme. It has a simple interface and can work with different types of cameras, including scintillator-based cameras and direct detection cameras, such as K2 Summit and DE cameras.
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.
Provides assistance in routine microscopy tasks on JEOL microscopes. JAMES provides a standalone platform that aims to ease: (i) repetitive procedures, (ii) prototype new image collection protocols and; (iii) optimize data quality. Additionally, the application can be run in conjunction with the EMEN software to query the microscope for relevant metadata and upload it in an automated way when acquiring images.