ProjectCryoET

Chair for Computer Aided Medical Procedures & Augmented Reality
Lehrstuhl für Informatikanwendungen in der Medizin & Augmented Reality

Developing Image Processing Techniques for Cryo Electron Tomography

Developing Image Processing Techniques for Cryo Electron Tomography

In medical collaboration with:
Deutsches Zentrum für Neurodegenerative Erkrankungen e.V.

Scientific Director: Nassir Navab

Contact Person(s): Shadi Albarqouni

Keywords: Reconstruction, Molecular Imaging, Machine Learning for Medical Applications, Microscopic Image Analysis

Abstract

Cryo-ET has recently emerged as a leading technique to investigate the three-dimensional(3D) structure of biological specimens at close-to-native state. It also bridges the gap between low-resolution imaging techniques (e.g. light microscopy) and high-resolution techniques (e.g. single particle electron microscopy). The technique consists of acquiring many two-dimensional (2D) projections of the structure under scrutiny at various tilt angles under cryogenic conditions. The 3D structure is recovered through a number of steps including projection alignment, reconstruction and de-nosing. The resolution of the reconstructed tomogram, however, is a affected by the low signal to noise ratio (SNR) of the projection images (typically 0.1 to 0.01) and the limited angular coverage (typically 60  to 70 ) resulting in wedge-shaped missing information in Fourier space, the so-called missing wedge; making the reconstruction process very challenging and demanding.

Team

Contact Person(s)

Shadi Albarqouni
M.Sc. Shadi Albarqouni

Working Group

Maximilian Baust
Dr. Maximilian Baust
Shadi Albarqouni
M.Sc. Shadi Albarqouni
Tobias Lasser
PD Tobias Lasser

Location



Technische Universität München
Institut für Informatik / I16
Boltzmannstr. 3
85748 Garching bei München

Tel.: +49 89 289-17058
Fax: +49 89 289-17059
Visit our lab at Garching.



internal project page

Please contact Shadi Albarqouni for available student projects within this research project.

The following presentation is a simple overview of the whole image processing pipeline in CryoET?.

Project Phases

Date Topic Conducted by Materials
Feb. 2014 Gradient Projection for Regularized Cryo-Electron Tomographic Reconstruction   CMMI-MICCAI Paper
Oct. 2014 Image Denoising in High Dimensional Space MLMI Group Project webpage
Feb. 2015 Multi-scale Graph-based Guided Filter for De-noising Cryo-Electron Tomographic Data (MG2F) Shadi BMVC Paper, BMVC Poster, Toy Example
Jun. 2015 RISE Internship Claire TBA


Edit | Attach | Refresh | Diffs | More | Revision r1.5 - 01 Sep 2015 - 11:42 - ShadiAlbarqouni

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