View All Electron Microscopy at Instruct
View All Data Analysis at Instruct
The EMBL Imaging Centre (IC) is a service unit in Heidelberg, Germany for high-resolution electron and light microscopy imaging, aiming at making cutting-edge workflows and technologies available to the international research community. We provide researchers from Europe and beyond with a synergistic portfolio of imaging services including electron microscopy/tomography, super-resolution and intravital microscopy to enable new ground-breaking research that crosses the scales of biology.
As part of our service, the EM service team of the IC provides Instruct projects with expertise in image processing of cryo-electron microscopy (cryo-EM), cryo-electron tomography (cryo-ET), and cryo volume scanning electron microscopy (cryo-FIB-SEM) data. We will assign required computational resources and personnel to support the projects in generating high-quality structural data.
For cryoFIB-SEM datasets, we offer automated data preprocessing which includes stack alignment, artifact removal (de-striping), and denoising. Specifically, for stack alignment we use SIFT or AMST-based approaches. Artifact removal and denoising is performed using VSNR and local adaptive histogram equalization (CLAHE filtering).
For cryo-EM analysis projects, we offer preprocessing of datasets collected on Glacios and Krios transmission electron microscopes. This includes on-the-fly preprocessing. Additionally, we offer support with single-particle analysis, support for model building, validation and deposition, and introduce users to required specialized software including Relion, CryoSPARC, and ChimeraX
For cryo-ET analysis projects, we offer preprocessing of datasets collected on Krios transmission electron microscopes. This includes automated on-the-fly tomogram reconstruction and denoising. Additionally, we introduce users to required specialized software including Relion, ChimeraX, Dragonfly or AreTOMO.
EMBL IC offers personalized support and computational resources needed for single-particle cryo-EM data processing, reconstruction and preprocessing of cryo-ET tomograms, and stack-alignment of cryoFIB-SEM datasets. More information on used software can be found at the respective documentations of each software:
Availability: yes
Physical access: yes
Remote access: yes
Average time of a visit: project dependent
