Life Sciences projects

Neurophotonics

We address neuroscience questions through functional imaging. We develop tools with roots in physics, biochemistry, optics, mathematics and nanofabrication and we're interested in how brain cells work on every level, from biophysical principles to consequences in behavior and from subcellular compartments to complete organisms. Our lab is in its startup phase and we will have exciting projects that offer one or a combination of the following activities: Optical engineering, mechanical engineering, genetic engineering, nano-engineering; programming; cell culturing and imaging. 

Membrane Voltage Nanoscopy

To optically read out membrane voltage from subcellular components like dendritic spines, we will use plasmonic enhancement of the fluorescence of a voltage sensitive protein. In this project, we will design plasmonic nanoantennas to enhance the fluorescence of a specific voltage sensor, fabricate samples of these antennas and culture cells on them expressing the voltage sensing protein, to test the premise of plasmonic enhancement of voltage sensitive fluorescence.

A compact multimodal two-photon microscope

Optogenetics allows for perturbation of cell signaling with fine spatial and temporal resolution. A good optogenetic microscope is a flexible instrument that does not only allow two-photon deep tissue imaging, but also multimodal perturbation. This puts constraints on miniaturization and fabrication on these devices. In this project, we will work on the design of a miniaturized version of a multimodal 2Pmicroscope.

Absolute voltage imaging

Absolute voltage imaging would allow new applications of optical voltage detection in for instance developmental biology. In this project, we will work on encoding membrane voltage in the fluorescence lifetime of a voltage sensors. We will create a new family of Förster Resonance Energy Transfer – based Genetically encoded voltage indicators and test their brightness and voltage sensitivity.

Timing escape times of photons

The group has built a unique microscope that can determine the time it takes for photons to escape from a material. The photons are generated when an electron beam hits a (nano)particle. The escape time bears unique knowledge about the particle and its local environment. The student is asked to do experiments to measure photon escape times from nanoparticles in different environments.

Light and electron microscopy

We use light and electron microscopy to study how the brain develops.  Our goal is to develop tools to image synapse function and structure in living zebrafish embryos, and connect this to nanoscale maps made using correlative photon and electron techniques.

3D Reconstructions of individual neurons

Neurons in the brain are the most complex cell types in the entire body. We use sparse fluorescence labelling techniques to visualize individual neurons developing in the zebrafish. Neurons can then be imaged by light microscopy techniques, like confocal laser scanning and light sheet microscopy.  From images of the same neuron on different days of development, we want to quantify changes in the shape of the neuron. For this project, we are using the latest generation of 3D neuron tracking and volume rendering softwares.

Tissue staining for light and electron microscopy

While electron microscopy can obtain spatial resolution of a few nanometers, light microscopy offers more options to obtain information about biological content of tissue. The two techniques can be combined in correlative light-electron microscopy, but some trade-offs exist: standard stains to obtain the best contrast in electron microscopy typically destroy fluorescence for light microscopy. We are testing staining protocols in zebrafish tissue to optimize visualization of synaptic structures with both light and electron imaging modalities.

Integrated Microscopy (photon and electron technology)

All microscopes have limitations, which hinders us in studying materials and understanding diseases. We try to push these limitations with Integrated Microscopy: new instruments and techniques based on physically integrating photon and electron technology. Our aim is to develop higher resolution, higher content, and higher throughput microscopy techniques and show their application in relevant biomedical and nanophotonic scientific research.

Building a Google Maps for the brain

To understand connectivity of the neural network in the brain, imaging with resolution below 10nm is necessary. This can be done with electron microscopy, but requires years of imaging time. We are developing new techniques based on parallel scanning with multiple beams, integration of light and electron microscopy, and use of artificial intelligence to allow fast, high-resolution imaging over multiple length scales. In this way we want to build a “Google Maps” for life, zooming in and out on brain from millimetres to molecules.

Timing escape times of photons

The group has built a unique microscope that can determine the time it takes for photons to escape from a material. The photons are generated when an electron beam hits a (nano)particle. The escape time bears unique knowledge about the particle and its local environment. The student is asked to do experiments to measure photon escape times from nanoparticles in different environments.

New super-resolution techniques to see proteins in tissue

Electron microscopes have a resolution of a few nanometers, but in the grayscale images molecules such as proteins cannot be seen. We are inventing new techniques to highlight proteins and other biological molecules in color at very high resolution and we collaborate with microscopists in medical centers to apply these techniques on their tissue samples. We have several student projects that can involve construction and design of experimental set-up, experimental work, data analysis, and programming.

Optical tomographic techniques

Optical tomographic techniques are applied in various areas ranging from hospitals to manufacturing facilities. In my team we develop novel optical tomographic techniques for imaging and sensing. We do this by modeling the physical imaging/sensing process using computational techniques, apply it for image construction or quantitative sensing, and implement it in hardware in the lab. If you like the combination of signal processing, computer simulations and experimental work combined in a single project than optical tomography may just be something for you.

Optical coherence tomography

Optical coherence tomography (OCT) is a highly successful biophotonic imaging technique that can make 3D images with micrometer resolution up to a few millimeters deep in tissue. It is based on low-coherence interferometry in a reflection geometry. We have state-of-the-art commercial and home-built OCT systems. We apply OCT imaging to study fluid flow, perform particle sensing, image plants and integrated circuits. Based on your interest and expertise there are multiple options for undergraduate (BEP) or graduate (MEP) projects. 

Optical tomography

In optical tomography 3D images of small animals such as zebrafish are made from projections of the optical attenuation, refractive index or fluorescence emission. The image reconstruction is based transmitted light, which makes the mathematics of the reconstructions more challenging. For obtaining high quality reconstruction of the tomographic images requires in-depth knowledge of the physics of the imaging process and the numerical reconstruction methods.  We have undergraduate (BEP) or graduate (MEP) projects on the theoretical side (simulations) and experimental side.

 

 

 

Computational Microscopy

Our field of work is Computational Microscopy; this comprises the combination of imaging physics and image processing to surpass fundamental limitations imposed by physics on image formation. My main application area for this research is in life sciences at the molecular level. We have projects for students interested in programming, image processing and simulations as well as theory development in single molecule localization microscopy, but also in building microscopy setups on an optical table with adaptive optics, advanced polarization optics and liquid nitrogen cooling.

Waveguide-based super-resolution at cryogenic temperatures

With this experimental project we aim to combine an optical waveguide with super-resolution imaging of single emitters at cryogenic temperatures. Light from the waveguide is coupled out via the evanescent field into a very shallow layer of the sample of about 200 nm, allowing seeing only the surface of the sample with high contrast. The cryogenic temperature allows to collect 100x more photons from single molecules than at room temperature. The project comprises of the design and implementation of the setup, as well as the measurements. (Bernd Rieger)

Optical super-resolution microscopy

The Nobel Prize in Chemistry 2014 was awarded for the development of superresolution microscopy, because it enables to record details about one order of magnitude below the diffraction limit of light. This limit (~250 nm) has been carved in stone for about 100 years, but has eroded over the last 10 years. We want to push this limit even further by more advanced image processing methods and optical setups. (Bernd Rieger & Sjoerd Stallinga)

Image processing for Electron Microscopy Tomography

We work on Electron Tomography for the next generation of Integrated Circuits (IC). Images obtained from 3D TEM reconstructions of ICs are required by the chip manufacturers to inspect the devices and find faults in the production process. These faults are very costly due to downtime of the production process and must be found in an automated fashion as quickly as possible. We employ advanced image analysis techniques in combination with knowledge about image formation and reconstruction to achieve this goal. (Bernd Rieger)

Whole slide scanning for digital pathology

Digital pathology is an emerging clinical practice in which a pathologist makes a diagnosis by examining a digital high-resolution image of a tissue slide. These images are acquired with a high-throughput automated microscope ("whole slide scanner"). We develop efficient optical quality testing methods for inspection of manufacturing quality and for monitoring systems during their operational lifetime, we work on new ways for scanning multiple focal slices simultaneously, and we investigate image analysis algorithms for diagnostic assistance. (Sjoerd Stallinga)

Structured illumination microscopy

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. Thedesign of illumination patterns in combination with various ways of scanning these patterns and image analysis methods can improve light efficiency and robustness. (Sjoerd Stallinga & Bernd Rieger)