Instruct Centre ES hosts the Instruct Image Processing Center (I2PC) and the Instruct Cryo-EM CNB – CSIC facility, working together to provide support to the Structural Biology Community. Find more on the Spain centre and apply to access the available technologies here.

 

 

 

This is an innovative approach for image processing of challenging samples presenting a large degree of flexibility, especially if this flexibility is continuous, making it difficult to assign images to discrete classes. As with other I2PC services, it uses the SCIPION framework, which includes movie alignment, particle picking, classification 2D-3D, volume reconstruction and atomic structure determination; however, the added value is the use of the newly developed “Flexibility Hub” module. This allows the interoperation among several recent methods for flexibility analysis, including the I2PC developed Zernike3D approach. SCIPION provides a multi-package workflow-oriented platform bridging several software suites like Xmipp, EMAN, Spider, Relion, CryoSparc, Bsoft, Frealign, ctffind and cryoDRGN, among others. More information about SCIPION can be found here. 

 

In the CNB Cryo-EM facility, the staff has worked the whole year in setting up the recently acquired infrastructure for cryoelectron diffraction and cryocorrelative techniques. The techniques are ready and have been first opened for the national community. These new techniques will be offered to Instruct in 2023.

 

 

 

Cryo-electron Tomography is a rapidly growing technique that can visualise cell organelles and biological macromolecules in their cellular context. Image processing algorithms allow the identification of the macromolecules of interest in the electron tomograms. Then, by extracting small subtomograms around those locations and identifying those similar particles, we may average them and recognise their different conformations. This latter process is called subtomogram averaging and has allowed solving a growing number of macromolecules with a resolution between 20-3A. 

The course aims were to provide a comprehensive overview of the whole image processing pipeline in Electron Tomography (ET) from the movie alignment of the tilt series, 3D reconstruction of the tomogram, particle identification, and subtomogram averaging, all inside Scipion integration framework.

CryoET is one of the most promising structural techniques and bridges the gap between structural and molecular biology and cell biology; the attendees of this course have now had an in-depth approach to this technique, guided by the I2PC team. This new knowledge will open new doors for them to new positions around the world. 

 

 

Hands-On Training Course that introduces the fundamentals and main tools needed to build an atomic model in the context of cryo-EM, starting from a 3D map and the aminoacid sequence of each protein chain. The tools used were within the framework of Scipion (de la Rosa-Trevin et al., 2016), and the examples focused mainly on the homology modeling scenario, including AlphaFold2 prediction models. 

 

 

The aim of the course was to provide an overall overview of image processing in single particle analysis (SPA).