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Precise to the nanometer

The position of stochastically blinking fluorescent molecules can be measured with nanometer precision from a movie acquired with a conventional widefield microscope. A super-resolution image can be reconstructed from the localization data, thereby circumventing the classical diffraction barrier to resolution. We develop new imaging modalities in this area (measuring emission colour and molecular orientation along with emitter position) and work on image analysis methods for image quantitation, for establishing performance limits, and for optimizing image acquisition and reconstruction protocols.
The image shows the effect of the density of labels and the precision with which they are localized on image resolution. See our Nature Methods paper for more information.
Interested in a BSc or MSc end project? We always have student projects available. Contact me by email or simply walk into my office (F266).
If you are looking for a PhD or PostDoc position, write an email with your CV and a motivation letter. We are always looking for enthousiastic young people wanting to advance science and technology!

Current team

Shining light

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. The design of illumination patterns in combination with various ways of scanning these patterns and image analysis methods can improve light efficiency and robustness.

 

PhD Theses

Christiaan Righolt
"Quantitative Microscopy to Measure the Nuclear Architecture"
Robert Nieuwenhuizen
"Quantitative Image Analysis for Single Molecule Localization Microscopy"
Carlas Smith
"Optimum Single Molecule Localization Microscopy"
Nadya Chakrova
"Versatile Structured Illumination Microscopy"
Mojtaba Shakeri
"Whole Slide Imaging Systems for Digital Pathology"
 

Pathology going digital

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.

The top image shows an example of an image taken with our whole slide scanning setup, the bottom images show a measurement of the through-focus Modulation Transfer Function and Phase Transfer Function.

Collaborators

I have worked or are working together with:

 

- I have a long-running collaboration with Bernd Rieger on super-resolution microscopy.
- David Grünwald, RNA therapeutics Institute, University of Massachusetts
- Erik Manders, Van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam
- Kees Jalink, Netherlands Cancer Institute, Amsterdam
- Sabine Mai, Genomic centre for cancer research and diagnosis, University of Manitoba
- Adriaan Houtsmuller, Erasmus Medical Center, Rotterdam
- Mark Bates, Max-Planck-Institute for Biophysical Chemistry, Göttingen
- Arno van Leenders, Erasmus Medical Center, Rotterdam
- Peter Török, Imperial College, London
- Bas Hulsken, Philips Digital Pathology, Best, The Netherlands
- Rene Berlich, Fraunhofer Institute, Jena

Alumni

- Luuk Balkenende, "Optimum metric for 2D data fusion in localization microscopy" (BSc, 2017)
- Cyrus Tirband Dasgerdi, "2D localization with a vector PSF model" (BSc, 2017)
- Marijn Siemons, "High precision wavefront control for 4D PSF engineering" (MSc, 2017)
- Mojtaba Shakeri, "Whole slide imaging systems for digital pathology" (PhD, defense 26-1-2017) Collaboration with Philips Digital Pathology in Cyttron II consortium
- Nadya Chakrova, "Versatile structured illumination microscopy" (PhD, defense 23-1-2017) Collaboration with Bernd Rieger in STW-perspectief consortium on optical nanoscopy
- Carlas Smith, "Optimum single molecule localization microscopy" (PhD, defense 12-9-2016) Collaboration with David Grünwald (University of Massachusetts) and Bernd Rieger
- Jim Winkens, " Automated classication of prostate cancer histology images using ConvNet feature extractor" (BSc, 2016)
- Robert Nieuwenhuizen, "Quantitative image analysis for single molecule localization microscopy" (PhD,  defense 12-1-2016, cum laude) Collaboration with Bernd Rieger in STW-perspectief consortium on optical nanoscopy
- Max Huisman, "Plenoptic Microscopy 2.0" (MSc, 2014)
- Douwe Scholma, "Fluorescence illumination box" (BSc, 2014)
- Marijn Siemons, " Resolution and Anisotropy in 3D Localization Microscopy" (BSc, 2014)
- Christiaan Righolt, "Quantitative microscopy to measure the nuclear architecture" (PhD, defense 16-5-2014) Collaboration with Sabine Mai (University of Manitoba) and Lucas van Vliet
- Khinsam Ly, " The effect of optical aberrations on the accuracy and precision of identifying point emitters" (BSc, 2014)
- Leon van der Graaff, "Fluorescence illumination box" (BSc, 2013)
- Jordi Broeken, "Simultaneous position and colour measurement in localization microscopy" (MSc, 2013)
- Farzad Fereidouni (PostDoc, 2013)
- Martijn Starmans, " Activation cycles of stochastically blinking molecules in super-resolution microscopy " (BSc, 2013)
- Sjoerd Verhoeckx, "Adding a dimension to localization microscopy" (MSc, 2013)
- Osman Atabey, " Extraction of point emitters in a 3D-Image using segmentation methods" (BSc, 2012)
- Robert Nieuwenhuizen, " Resolution in Localization Microscopy " (MSc, 2011, cum laude)
- Roel Obdam, " Sub-diffraction-limit localization of two blinking emitters" (BSc, 2011)
- Jordi Broeken, " Precise to the nanometer: eliminating model errors" (BSc, 2010)
- Erick Webbe, " Plenoptic Imaging Systems " (MSc, 2010)
- Ron Schutjens, " Signal to background ratio for fluorescence microscopy systems" (BSc, 2009)