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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.

EMHP / Electron Microscopy Hole Punch

Allows users to focus on streamlining this preprocessing stage. EMHP works on image assessment, masking, and pick filtering in preparation for single particle analysis. This tool contains an algorithm for detecting carbon supports in cryo-EM images. Thanks to this algorithm, users are able to preprocess their data rapidly and with minimal overhead while providing results in a format readable or easily converted. This package includes especially a Tkinter-based GUI image assessor.

RELION / REgularised LIkelihood OptimisatioN

Employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). RELION is implemented as a stand-alone program, and its open-source C++ code is available for download. Application of RELION to both simulated and experimental data illustrates that reconstructions that are free from overfitting may be obtained in a highly objective manner, without compromising reconstruction quality and at acceptable computational costs.


Provides an image processing environment with a particular emphasis on transmission electron microscopy (TEM) structure determination. SPARX includes a graphical user interface that provides a complete graphical programming environment with a data/process-Xow infrastructure, an extensive library of Python scripts that perform speciWc TEM-related computational tasks, and a core library of fundamental C++ image processing functions. In addition, SPARX relies on the EMAN2 library and cctbx, the open-source computational crystallography library from PHENIX. The design of the system is such that future inclusion of other image processing libraries is a straightforward task. SPARX and all dependencies are free for academic use and available with complete source.

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.