Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8537808 | PMC |
http://dx.doi.org/10.3390/molecules26206224 | DOI Listing |
J Struct Biol
December 2024
Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain. Electronic address:
Cryo-electron tomography is an imaging technique that allows the study of the three-dimensional structure of a wide range of biological samples, from entire cellular environments to purified specimens. This technique collects a series of images from different views of the specimen by tilting the sample stage in the microscope. Subsequently, this information is combined into a three-dimensional reconstruction.
View Article and Find Full Text PDFJ Struct Biol
March 2024
Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain. Electronic address:
Electron tomography is an imaging technique that allows for the elucidation of three-dimensional structural information of biological specimens in a very general context, including cellular in situ observations. The approach starts by collecting a set of images at different projection directions by tilting the specimen stage inside the microscope. Therefore, a crucial preliminary step is to precisely define the acquisition geometry by aligning all the tilt images to a common reference.
View Article and Find Full Text PDFMicromachines (Basel)
September 2023
Spanish National Centre for Biotechnology, Spanish National Research Council, Calle Darwin, 3, 28049 Madrid, Spain.
Cryogenic electron microscopy (Cryo-EM) has been established as one of the key players in structural biology. It can reconstruct a 3D model of a sample at a near-atomic resolution. With the increasing number of facilities, faster microscopes, and new imaging techniques, there is a growing demand for algorithms and programs able to process the so-called movie data produced by the microscopes in real time while preserving a high resolution and maximal information.
View Article and Find Full Text PDFJ Struct Biol
December 2023
Centro Nac. Biotecnologia (CSIC), c/Darwin, 3, 28049 Cantoblanco, Madrid, Spain. Electronic address:
Single Particle analysis (SPA) aims to determine the three-dimensional structure of proteins and macromolecular complexes. The current state of the art has allowed us to achieve near-atomic and even atomic resolutions. To obtain high-resolution structures, a set of well-defined image processing steps is required.
View Article and Find Full Text PDFBrief Bioinform
May 2022
College of Computer Science and Engineering, Northwest Normal University, 730070, Lanzhou, China.
Single-particle cryo-electron microscopy (cryo-EM) has become one of the mainstream technologies in the field of structural biology to determine the three-dimensional (3D) structures of biological macromolecules. Heterogeneous cryo-EM projection image classification is an effective way to discover conformational heterogeneity of biological macromolecules in different functional states. However, due to the low signal-to-noise ratio of the projection images, the classification of heterogeneous cryo-EM projection images is a very challenging task.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!