I2PC - Instruct Image Processing Center

Instruct Image Processing Center

Services

Image analysis service: The center provides support to structural biologists wanting to extract 3D structures from their micrographs. The center can handle single particles data, 2D crystallographic data, helical particles data, icosahedral particles data, electron tomographic data, and X-ray tomographic data.
Image processing support:The center solves questions about the best image processing workflow for a particular imaging problem.
Software support: the center provides support on the use of the software packages managed by the center itself (Scipion and Xmipp).
Standardization of image processing workflows: the center acts like a hub in the definition of standardized workflows for image processing in the different imaging modalities (single particles, 2D crystals, icosahedral particles, helical particles, electron tomography, X-ray tomography). The center also constructs an ontology of image processing steps, maintains a portal of geometric conventions, and defines points of interchange between different software packages.
Construction of ad hoc programs: the center writes the necessary programs to execute the previously defined workflows as well as any ancillary program needed to connect different software packages.

Ongoing Projects

Xmipp, "X-Window-based Microscopy Image Processing Package", is a suite of image processing programs, primarily aimed at single-particle 3D electron microscopy.
3D Electron Microscopy Benchmark website, a joint initiative of the National Institute of Bioinformatics (INB) and the INSTRUCT Center for Image Processing in Microscopy, has been develop to foster the development of new advanced methods in the area of image processing in Structural Biology. To this end we provide a robust computational infrastructure capable of supporting the automatic and standardized benchmarking of image processing applications.
Scipion is an image processing framework for 3D EM. It integrates several software packages for the elucidation of 3D structures and allows the execution of image processing workflows. Additionally, processes can be detailedly traced and carefully automatically reproduced.
PeppeR is the Java based, graphical 3D-EM DAS client, intended for visualization of 3D-EM volume maps, plus atomic resolution structures from fitting experiments, together with their annotations.
3D Electron Microscopy Methods Wiki is an extensive repository of three-dimensional electron microscopy (3DEM) methods.
Conventions for Data Interchange in 3D Electron Microscopy documents whether the map files produced in a particular package are consistent with the 3DEM conventions. It publishes the conventions and assumptions followed by each EM package.