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Interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner, while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions. The rapid detection of any errors that may occur greatly increases the productivity of recording sessions at the electron microscope.


High Performance Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, China; National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

AIR Tools / Algebraic Iterative Reconstruction Tools

Assists in calculating regularized solutions to discretization of inverse problems. AIR Tools aims to provide easy-to-use implementations of the most important algebraic iterative reconstruction (AIR) methods. Each method is equipped with several stopping rules as well as heuristics for choosing the relaxation parameter. It is written for numerical analysts and application specialists who want to experiment with the iterative methods and their convergence properties.

TOM Toolbox

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.


Provides the essential tools for the analysis of subtomograms obtained by cryo electron tomography. PyTom covers a processing pipeline of tomogram reconstruction, localization of macromolecular complexes in tomograms, fine alignment of subtomograms extracted at these locations and their classification. PyTom is mostly written in Python making it fairly easy to add new functionality as well as to customize existing methods for specific purposes. The package is mainly developed in the Förster lab at the Max Planck Institute for Biochemistry, but developers are highly encouraged to contribute to PyTom on an open source basis.

STIR / Software for Tomographic Image Reconstruction

Provides a Platform-independent Object-Oriented framework for all data manipulations in tomographic imaging. STIR can be used to study existing and/or new reconstruction algorithms for a wide variety of cylindrical scanners. It enables the research community to study the performance of several algorithms on Single Photon Emission Computed Tomography (SPECT) data, and potentially implement new algorithms by expanding the existing framework. The tool offers the prospect to compare different Positron Emission Tomography (PET) scanners using identical correction and reconstruction software.

PEET / Particle Estimation for Electron Tomography

Serves for microtubule-kinesin motor domain complexes. PEET is a program that can align particles in 3-D subvolumes extracted from tomograms. This tool seeks the optimal alignment of each particle against a reference volume through several iterations. The program utilizes the parallel processing framework within IMOD software, and the lengthy computations can be distributed to multiple cores on one computer, to a set of linked workstations, or to a cluster.

RAPTOR / Robust Alignment and Projection Estimation for Tomographic Reconstruction

Aligns tomographic tilt series obtained from electron microscopes. RAPTOR is intended to automatically obtain a full-precision alignment comparable to the one obtained with extended manual intervention. Fiducial particles are needed in the image for the alignment. RAPTOR has been tested in many different datasets (cryo-EM, plastic, thick sections) and has given good results. RAPTOR has been incorporated into IMOD.

Amira 3D Software for Life Sciences

Allows users to visualize, manipulate, and understand data from imaging modalities such as computed tomography, microscopy or Magnetic resonance imaging (MRI). Amira 3D Software for Life Sciences provides features to import and process 2D and 3D images data, visualization techniques and tools for visual analysis. Users can also create and share presentations. The base product can be customized by adding functional extensions to fit special needs in different application areas.