Abstract
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.
Highlights
Xmipp is a software package for cryo-electron microscopy (Cryo-EM) and electron tomography (ET), available as a standalone project or via Scipion [1] framework
We helped with the evaluation of the Map Challenge [25] and we proposed a pair comparison method to sort reconstructions based on a figure of merit [26]
We showed that the combination of deep learning and the classical projection matching approach could lead to improved reconstructions while decreasing the computational time
Summary
Xmipp is a software package for cryo-electron microscopy (Cryo-EM) and electron tomography (ET), available as a standalone project or via Scipion [1] framework. It offers multiple programs for almost all steps of the typical single particle analysis (SPA) processing pipeline and several programs for ET. Xmipp is still providing some crucial functionality to Scipion and many auxiliary protocols that can be used in the processing pipeline of the Scipion project. This article provides an overview of the work of the Biocomputing Unit of the CNBCSIC, Madrid, concerning Xmipp. The last section summarizes our contribution to Cryo-EM, ET, and SPA in the last eight years and discusses possible future directions of the research
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