Student Projects

The objective of this project is to develop automatic quality masurements on CT colonography data and relate this to the quality assessments done by radiologists. Contact: Frans Vos, Lucas van Vliet Documentation: CT colonography: automatic assessment of image quality

  TU Delft is developing sophisticated methods for electronic cleansing, i.e. image processing algorithms to automatically segment the colon surface from the CT data, prior to visualization. The objective of this project is to develop a polyp detection algorithm that is integrated into our methods for electronic cleansing. Contact: Frans Vos, Lucas van Vliet Documentation: CT colonography: An integrated system for automated cleansing and polyp detection

  This project aims to automatically indentify salient points in which the registration is optimal, after which the differences between Alzheimer patients and controls are to be studied. Contact: Frans Vos, Lucas van Vliet Documentation: Diffusion Tensor MRI: Automatic detection of characteristic points

  This project aims to study the evolution over time of DTI parameters along relevant white matter tracts, e.g. by means of a 4D Principal Component Analysis. Contact: Frans Vos, Lucas van Vliet Documentation: Diffusion Tensor MRI: 4D analysis of Alzheimer’s disease

  Dynamic Contrast Enhanced MRI visualizes the dynamic response of tissue to the inflow of blood. This project aims to automatically identify inflammatory tissue in patients suffering from Crohn’s disease in order to quantify disease activity. Contact: Frans Vos, Lucas van Vliet Documentation: Dynamic Contrast Enhanced (DCE) MRI: automatic classification

Conventional X-ray imaging relies on local variations in absorption. The slight deviation in refractive index from unity gives rise to refraction and diffraction of X-rays, using this effect in phase contrast imaging holds the promise of improved contrast of soft tissues. Advancing this technique requires table-top sized high brightness sources, and innovations in image acquisition and processing. We explore different methods for source evaluation, tomographic reconstruction and disentanglement of attenuation and phase. Contact: Sjoerd Stallinga, Lucas van Vliet

The fluorescence of Quantum Dots switches on/off at random. Some molecules can be manipulated to do so as well. This stochastic switching, “blinking”, can be used to localize single emitters with nanometer precision, well below the limits of conventional microscopy. We explore different methods of reconstruction in order to push the limits of this technique. Contact: Bernd Rieger  

Localization of single emitters for nanoscopy relies on accurate and precise fitting of the observed image spot to a model Point Spread Function. Often used simple models neglect many relevant effects, such as the different optical aberrations. We investigate the trade-odd between rigorous PSF-modeling and efficient spot fitting. Implementation of algorithms is done on GPUs. Contact: Bernd Rieger, Sjoerd Stallinga

The study of viruses and small sub-cellular components requires an increase in the resolution of 3D cryo-electron tomography. We use forward modeling of the image formation process based on parameters that are estimated from the sample itself to achieve the resolution goals.  Contact: Bernd Rieger  

An intriguing way to make a 3D fluorescence image is to record a set of (2D) images on a camera for a set of specifically designed illumination patterns. As a bonus the in-plane resolution can be doubled as well. We look for ways to optimize the number and type of illumination patterns by applying algorithms from the field of Compressive Sensing and by adapting the patterns to the recorded image content so far.  Contact: Bernd Rieger, Sjoerd Stallinga Documentation: Student projects on programmable illumination.pdf

A Programmable Array Microscope is a fluorescence microscope augmented with a Spatial Light Modulator, a pixilated device for projecting arbitrary illumination patterns on the sample.  We look for students who wish to work on the experimental implementation of the different ideas on the use of illumination patterns in microscopy. Contact: Bernd Rieger, Sjoerd StallingaDocumentation: Student projects on programmable illumination.pdf

A plenoptic microscope can make a 3D-image of an object using only a single image obtained with a 2D image sensor. This remarkable feat is achieved by introducing an array of micro-lenses in front of the image sensor for capturing image information as a function of position in the imaged field and as a function of the direction of view. This enables a 3D reconstruction of the image, but at the expense of a loss in lateral resolution. We explore methods for recovering this loss by combining alternative optical designs and super-resolution reconstruction via the use of a priori object information. Contact: Sjoerd StallingaDocumentation: Student projects on super-resolution in plenoptic microscopy.pdf

The technique of FISH (Fluorescence In-Situ Hybridization) uses fluorescently labeled gene markers for measuring the (over)expression of certain genes. These labels show up as dots in the images, and the image analysis task consists of counting the dots per cell. We investigate the role of the microscope Numerical Aperture in the reliability of this task. This is of significance for fully automated, high-speed scanning and analysis of tissue slides in the field of digital pathology. We look for students with both an interest in modeling and computer programming and in experimental research. Contact: Bernd Rieger, Sjoerd Stallinga

We study biophysical properties of DNA such as the diffusion constant and persistence length using Tethered Particle Motion (TPM). This method is also used in our group as a detection assay for target mRNA. To study the system on short time scale it is imperative to acquire images with high framerates. Motion blur otherwise hampers the adequate description of the dynamics. A solution is to use powerful burst illumination (microseconds) via LEDs in overdrive mode with a very low duty cycle. Contact: Bernd Rieger
Documentation: StudentPoster LEDverlichting.pdf

Influence of low-light conditions on estimation of FRET efficiencies and anisotropy measurements in fluorescent microscopy FRET results from the dipole-dipole interaction between two fluorophores, the emission spectrum of one (donor, D) overlapping the excitation spectrum of the other (acceptor, A). The strength of this interaction is dependent upon the D-A separation and is very sensitive in the 2-10 nm range. The ability of FRET to measure such distances has lead to widespread use of this technique in the study of molecular interactions and functional states in biological systems. But what happens to the uncertainty of the FRET level if only very little photons are recorded? Contact: Bernd Rieger  

Image analysis for scanning electron microscopy S(T)EM Images in Scanning Transmission Electron Microscopy and Scanning Electron Microscopy suffer from vibrations and distortions of the system. During the scan of the sample magnetic, acoustic and floor vibrations distort the electron beam and then in the end also the image. When resolutions are in the nanometer range even the smallest vibration distort the image and reduce useful information in the image.We want to increase the image resolution by post-processing of disturbed images. Possibility for internships at FEI Company. Contact: Bernd Rieger

Electron Tomography is an important technique that extends the unique structure resolution capabilities of the Transmission Electron Microscopy into three dimensions. This project investigates how image processing and analysis can help to answer the chemical questions on an automated, reproducible, and quantitative basis. Contact: Bernd Rieger
Documentation: uustudent.pdf

In many corneal studies, endothelial cell density and morphology is used to assess the quality of the cornea. Based on these parameters important therapeutic decisions are made, regarding for example surgical intervention and the corneal transplantation method (full thickness versus lamellar). The endothelium may be imaged by specular microscopy or by confocal scanners. Metrics that are employed include cell density, cell area size and its variation and cell shape and its variation. Contact: Bernd Rieger
Documentation: EyeHospital.pfd

Our aim is to perform single-cell studies with a dual-waveguide optical trap in a lab-on-a-chip environment. The project further includes simulations and experiments for estimating the trapping characteristics of the device.

Contact: Jaap Caro, Thijs van Leest
Documentation: Photonic fishing.pfd

Aim of the project is to use the evanescent field of a waveguide or a resonator, integrated in a fluidic channel, to optically trap and manipulate micrometer size particles. The project involves designing structures with simulation software and experiments with fabricated devices.

Contact: Jaap Caro, Thijs van Leest
Documentation: Photonic surfing.pfd