Strategic Technical Consulting and Product & Project Management for Electron-Microscopy Software


The Instruct Image Processing Center (I2PC) at the Spanish National Center for Biology (CNB), which belongs to the European Strategic Infrastructure Project (ESFRI) in the area of Structural Biology. I2PC provides support to structural biologists, helping them to maximize the extraction of biological knowledge from their microscopy images.


In the past few years, 3D electron microscopy (3DEM) has undergone a revolution in instrumentation and methodology. In this context, I2PC started to develop Scipion, an image processing framework for obtaining 3D models of macromolecular complexes using Electron Microscopy (3DEM). Scipion aims to address the problems of integration and interoperability in 3DEM. There is a commitment to provide state of the art algorithms and software to the EM community, including software from other groups. However, integration of open-source software from other international labs is a complex and difficult task both from a technical and scientific point of view. The heterogeneity of the software packages in terms of programming language, libraries and mathematical and structural biologies method requires a multidisciplinary team and makes quite difficult to estimate the time and the computational resources needed.


EyeSeeTea provided software development audits services to improve the development processes in this R+D project and project management. Currently, Scipion integrates several software packages and presents a unified interface for both biologists and developers. Scipion allows executing workflows combining different software tools while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on.

Scipion is widely used nowadays and several labs and organisations uses and contributes to it. The number of users and integrated protocols has increased dramatically and the coordination between the different center is much better than in the past years. Thanks to the project success, we are still collaborating with the Spanish National Center for Biotecnology in a wide ranges projects: developing and maintenance of the different websites, maintenance of the cluster infrastructure, server configuration, etc.

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