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AISB opportunities Bulletin Item

PhD position Cryo-Electron Tomographic reconstruction, Delft, The Netherlands

PhD position  Cryo-Electron Tomographic reconstruction

image processing, adaptive volumetric reconstruction, inverse problems, low-dose Cryo-TEM tomography

Research description
The goal of this project is to enable one nanometer resolution in 3D electron tomography image volumes of frozen biological specimen after reconstruction from a low-dose cryo-Transmission Electron Microscopy tilt series (TEM). This increases the resolution by a factor of 3 to 7 (dependent on imaging and sample condition), which is enormous in electron imaging where fractional increases by tens of percentages have been typical in the last three decades. The three physical road blockers to achieve this goal are: 1. limited irradiation dose; 2. local variations in the imaging conditions; 3. complex wave propagation through inhomogeneous media. The road blockers in terms of image processing are the resulting very bad
signal-to-noise ratio of about unity in the 2D projections and the lack of correct inclusion of the image formation in the reconstruction process. Simple reconstruction techniques like weighted backprojection fail to include the image different from absorption and
A first PhD student is already working towards the experimental data collection protocol based on low-dose statistics and the development of a new forward imaging model. In the second, still vacant, project we want to develop data-driven image processing strategies for noise suppression before and during regularization in reconstruction, while including a space-variant contrast transfer function correction.

The main research will be performed at the Quantitative Imaging Group in the department of Imaging Science & Technology of the Delft University of Technology. The actual electron tomograms are acquired at the Electron Microscopy section in the department of Molecular Cell Biology at Leiden University Medical Center. The whole project is part of a larger industrial partnership program with FEI Company in Eindhoven, The Netherlands, a world leader in electron microscopy.

The candidate must have a strong background in mathematics and hold a MSc. degree in Physics, Mathematics, Computer Science or Electrical Engineering. Experience with optics, image processing and reconstruction is desirable. Good programming skill are essential.

Conditions of employment
When fulfilling a PhD position at the FOM foundation, you will have an employee status and can participate in all the employee benefits FOM offers. You will get a contract for 4 years. Your salary will be up to a maximum of 2,457 euro gross per month.

Interested candidates should send a full CV and a motivation letter to

Further information
Dr. Bernd Rieger, +31(0)152788754, Lucas J. van Vliet, +31(0)152787989
Quantitative Imaging Group,	
Department of Imaging Science and Technology		
Faculty of Applied Sciences				
Delft University of Technology				
The Netherlands