Searched for: collection%3Air
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Nieuwenhuizen, R.P.J. (author), Nahidiazar, L. (author), Manders, E.M.M. (author), Jalink, K. (author), Stallinga, S. (author), Rieger, B. (author)
Co-localization analysis is a widely used tool to seek evidence for functional interactions between molecules in different color channels in microscopic images. Here we extend the basic co-localization analysis by including the orientations of the structures on which the molecules reside. We refer to the combination of co-localization of...
journal article 2015
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Nieuwenhuizen, R.P.J. (author), Bates, M. (author), Szymborska, A. (author), Lidke, K.A. (author), Rieger, B. (author), Stallinga, S. (author)
Quantification in localization microscopy with reversibly switchable fluorophores is severely hampered by the unknown number of switching cycles a fluorophore undergoes and the unknown stoichiometry of fluorophores on a marker such as an antibody. We overcome this problem by measuring the average number of localizations per fluorophore, or...
journal article 2015
document
Righolt, C.H. (author), Mai, S. (author), Van Vliet, L.J. (author), Stallinga, S. (author)
The quality of the reconstructed image in structured illumination microscopy (SIM) depends on various aspects of the image filtering process. To optimize the trade-off between resolution and ringing artifacts, which lead to negative intensities, we extend Lukosz-bound filtering to 3D SIM and derive the parametrization of the 3D SIM cut-off. We...
journal article 2014
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Righolt, C.H. (author), Slotman, J.A. (author), Young, I.T. (author), Mai, S. (author), Van Vliet, L.J. (author), Stallinga, S. (author)
Various aspects of image filtering affect the final image quality in Structured Illumination Microscopy, in particular the regularization parameter and type of regularization function, the relative height of the side bands, and the shape of the apodization function. We propose an apodization filter without adjustable parameters based on the...
journal article 2013
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Hulsken, B. (author), Vossen, D. (author), Stallinga, S. (author)
Array illuminators generating spots with high NA at high efficiency are presented. They are designed via application of high-NA scalar optics methods, and implemented as periodic binary phase structures. These array illuminators are used in a multi-spot scanning microscope for scanning large sample areas with a relatively high resolution.
journal article 2012
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Stallinga, S. (author), Rieger, B. (author)
We introduce a method for determining the position and orientation of fixed dipole emitters based on a combination of polarimetry and spot shape detection. A key element is an effective Point Spread Function model based on Hermite functions. The model offers a good description of the shape variations with dipole orientation and polarization...
journal article 2012
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Stallinga, S. (author)
A theory of optical trapping at low Numerical Aperture (NA) is presented. The theory offers an analytical description of the competition between the stabilizing gradient and destabilizing scattering force. The trade-off can be characterized by a single dimensionless trapping parameter, which increases with bead size to wavelength ratio ?/?, m,...
journal article 2011
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Voortman, L.M. (author), Stallinga, S. (author), Schoenmakers, R.H.M. (author), Van Vliet, L.J. (author), Rieger, B. (author)
Today, the resolution in phase-contrast cryo-electron tomography is for a significant part limited by the contrast transfer function (CTF) of the microscope. The CTF is a function of defocus and thus varies spatially as a result of the tilting of the specimen and the finite specimen thickness. Models that include spatial dependencies have not...
journal article 2011
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