2 PhD positions in cryo-Electron 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 road blockers to
achieve this goal are: 1. limited irradiation dose; 2. local variations
in the imaging conditions - not only lateral due to tilt, but also axial
due to sample thickness; 3. complex wave propagation through
inhomogeneous media. 
The first hampers all computations and requires dedicated image
processing that takes advantage of the local image structure and clever
regularization of the reconstruction process. The second requires
estimation of a space-variant contrast transfer function (CTF) in 3D
space to avoid a systematic error in the imaging model. The third causes
scattering of electrons which hampers the inverse problem in which we
compute a distribution of electron potential.
We have two interrelated research positions to overcome these problems
and achieve one nanometer resolution in tomograms. The first is directed
towards the experimental data collection protocol based on low-dose
statistics and the development of a new forward model which properly
accounts for a space-variant CTF and beam-sample interactions in
inhomogeneous media. In the second project we want to develop
data-driven image processing strategies for noise suppression before and
during regularization in reconstruction, while including a space-variant
CTF correction.

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

Keywords
low-dose Cryo-TEM tomography, adaptive volumetric reconstruction,
electron optics, CTF

Requirements
The candidate must have a strong background in physics and mathematics
and hold a MSc. degree in Physics, Mathematics, Computer Science or
Electrical Engineering. Experience with electron microscopy and optics,
image processing and reconstruction is desirable. 

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.

Information and application 
Dr. Bernd Rieger, +31(0)152788754, B.Rieger@tudelft.nl 
Prof.dr.ir. Lucas J. van Vliet, +31(0)152787989
Quantitative Imaging Group, www.ist.tudelft.nl/qi
Department of Imaging Science and Technology
Faculty of Applied Sciences
Delft University of Technology				
Lorentzweg 1
2628 CJ Delft, The Netherlands				

Dr.ir. A.J. Koster, +31(0)715269294
Section Electron Microscopy
Department of Molecular Cell Biology
Leiden University Medical Center www.lumc.nl/1050
2300 RC Leiden, The Netherlands