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Papers by Hans van der Voort

Research paper thumbnail of A 3‐D model for chromatin organisation of G1 and G2 populations from quantitative confocal image analysis

Cytometry, 1997

A study on the chromatin organisation of synchronised G1 and G2 populations of maize root cell nu... more A study on the chromatin organisation of synchronised G1 and G2 populations of maize root cell nuclei is reported using 3-D images acquired with a confocal fluorescence microscope. The analysis is based on the concept of accessibility. Accessibility of a position x is the effort to arrive at x, when choosing the minimum effort path to arrive at x from the nuclear border. The effort is then taken to be proportional to the amount of all mass encountered on the path, and computed by a technique called the grey valued distance transform. The approach relies heavily on quantitative analysis of the intensity information. Hence, considerable attention was paid to the quantitative modification of the confocal intensity values by diffraction, absorption and scatter corrections. Three texture features are extracted from the accessibility maps: the global object inaccessibility, the relative object accessibility, and the object homogeneity. On the basis of individual texture features, no distinction between the G1 and G2 populations could be established. However, the three features combined did show a clear difference with a high significance.

Research paper thumbnail of Fast volume render techniques for interactive analysis

The Visual Computer, 1997

Without graphics hardware, interactive volume rendering is almost impossible with the current gen... more Without graphics hardware, interactive volume rendering is almost impossible with the current generation of computers and software. We describe the implementation of a volume renderer for interactive analysis of confocal images. We propose several techniques to accelerate the rendering of grey-value volumes. We propose to illuminate the volume selectively with ray templates to get a proper shadow cue in the shortest feasible time. In the viewing phase, rendering is distinctively accelerated for four user interactions: (1) a total change by successive adaptive refinement, (2) an unknown change in the view with this refinement strategy combined with suspended interpolation, (3) a known change in the view by recalculating only that part and (4) a view translation by recalculating the uncovered part.

Research paper thumbnail of A quantative comparison of two restoration methods as applied to confocal microscopy

Research paper thumbnail of A quantitative comparison of image restoration methods for confocal microscopy

Journal of Microscopy, 1997

Research paper thumbnail of Three-deimensional visualization of multi-channel volume data: The amSFP algorithm

Research paper thumbnail of Image analysis in biology Edited by Donat-P. Häder CRC Press, Boca Raton (1992) ISBN 0-8493-6033-1; 256 pages, illustrated, $179.00

Research paper thumbnail of Avalanche photodiode detection with object scanning and image restoration provides 2–4 fold resolution increase in two‐photon fluorescence microscopy

Bioimaging, 1996

ABSTRACT High-quantum-efficiency photodetection, millisecond pixel dwell time stage scanning and ... more ABSTRACT High-quantum-efficiency photodetection, millisecond pixel dwell time stage scanning and image restoration by maximum-likelihood estimation are synergetically combined and shown to improve the resolution of two-photon excitation microscopy 2-4 fold in all directions. Measurements of the two-photon excitation point-spread function (PSF) of a 1.4 aperture oil immersion lens are carried out by imaging fluorescence beads with a diameter of one seventh of the excitation wavelength (830 nm) and subsequent deconvolution with the bead object function. The proposed method of resolution increase is applied to beads as well as to rhodamine labelled actin fibres in mouse fibroblast cells. As the resolution improvement is not based on the non-linear effect of two-photon excitation, the results imply a comparable resolution increase in single-photon excitation confocal microscopy. In the fibroblasts, we established a three-fold improvement in axial resolution, namely from 840 nm before, to 280 nm after restoration (full-width at half-maximum). Actin fibres with axial distances of 850 nm, otherwise difficult to discern, are fully separated. In the lateral direction, images of fluorescence beads of about 110 nm diameter are restored to the real dimensions of the beads with an accuracy of better than one pixel (41 nm).

Research paper thumbnail of Spectral Volume Rendering

Ieee Transactions on Visualization and Computer Graphics, 2000

ÐVolume renderers for interactive analysis must be sufficiently versatile to render a broad range... more ÐVolume renderers for interactive analysis must be sufficiently versatile to render a broad range of volume images: unsegmented ªrawº images as recorded by a 3D scanner, labeled segmented images, multimodality images, or any combination of these. The usual strategy is to assign to each voxel a three component RGB color and an opacity value. This so-called RGB approach offers the possibility of distinguishing volume objects by color. However, these colors are connected to the objects themselves, thereby bypassing the idea that in reality the color of an object is also determined by the light source and light detectors c.q. human eyes. The physically realistic approach presented here models light interacting with the materials inside a voxel causing spectral changes in the light. The radiated spectrum falls upon a set of RGB detectors. The spectral approach is investigated to see whether it could enhance the visualization of volume data and interactive tools. For that purpose, a material is split into an absorbing part (the medium) and a scattering part (small particles). The medium is considered to be either achromatic or chromatic, while the particles are considered to scatter the light achromatically, elastically, or inelastically. It appears that inelastic scattering particles combined with an achromatic absorbing medium offer additional visual features: Objects are made visible through the surface structure of a surrounding volume object and volume and surface structures can be made visible at the same time. With one or two materials the method is faster than the RGB approach, with three materials the performance is equal. The spectral approach can be considered as an extension of the RGB approach with a greater visual flexibility and a better balance between quality and speed. Index TermsÐVolume rendering, light/matter interaction, light spectra, physical realism, visual cues.

Research paper thumbnail of Abstracts of the 2nd European Super-Resolution User-Club Meeting

The 2 nd meeting of the Leica Super-Resolution User Club was held from September 25 to 27, 2012 i... more The 2 nd meeting of the Leica Super-Resolution User Club was held from September 25 to 27, 2012 in collaboration with the Science for Life Laboratory at the Karolinska Institute, Stockholm, Sweden. With a mixture of engaging talks by key experts in the field of super-resolution microscopy and stimulating discussion sessions, the meeting proved as popular as last year's event, attracting a wide range of scientists interested in both confocal and widefield super-resolution and sample preparation techniques.

Research paper thumbnail of Quantitative 3-D texture analysis of interphase cell nuclei

Proceedings., 11th IAPR International Conference on Pattern Recognition. Vol. IV. Conference D: Architectures for Vision and Pattern Recognition,, 2000

Research paper thumbnail of Thee-dimensional visualization methods for confocal microscopy

Journal of Microscopy

ABSTRACT

Research paper thumbnail of Confocal Scanning Laser Fluorescence And Reflection Microscopy: Measurements Of The 3-D Image Formation And Applications In Biology

Research paper thumbnail of Dimensional imaging of biological structures by high resolution confocal microscopy. Scanning Microscopy, 2, 33

Scanning microscopy

ABSTRACT

Research paper thumbnail of Chapter 14 Three-Dimensional Confocal Fluorescence Microscopy

Research paper thumbnail of Three-dimensional arrangement of Crepis capillaris in mitotic prophase and anaphase as studied by confocal scanning laser microscopy

Journal of Cell Science

To estimate the extent of ordering of chromosomes, confocal scanning laser microscopy-was used to... more To estimate the extent of ordering of chromosomes, confocal scanning laser microscopy-was used to make three-dimensional images from optical sections. For Crepis capillaris, which has 2n = 6 easily recognizable chromosomes, a statistically significant sample of 75 Feulgen-stained root tip anaphases was analysed. A comparison of the observed chromosome ordering and the expected random distribution showed a significant surplus of one of the arrangements with a juxtaposition of the two chromosomes with a nucleolus organizer region. Two of the arrangements with these chromosomes in opposite positions were never observed in our material. Another analysis of 30 mithramycin Astained prophases and 30 meta-and anaphases showed partly different patterns of non-random chromosome distribution in the two stages of mitosis. A preference for an association of the homologues was observed for all pairs of chromosomes in prophase cells, whereas in meta-and anaphase the association only persisted for the nucleolus organizer chromosomes. This indicates that there may be some relocation of the chromosome positions during the transition from prophase to metaphase. In meta-and anaphase one of the arrangements with juxtaposed NOR chromosomes was preferred, i.e. the ordering in which chromosomes 1 and 3 occupied alternate positions. Probably, the nucleolus is an important factor in producing a non-random distribution, but there could be other factors that influence chromosome ordering as well. A comparison of the anaphase chromosome ordering in C. capillaris plants from very different localities, indicated that the observed non-random distribution was independent of the origin of the material. Existing models of chromosome disposition are not sufficient to explain the observed non-random chromosome ordering in C. capillaris.

Research paper thumbnail of Illumination and detection strategies for confocal microscopy

Proceedings of SPIE - The International Society for Optical Engineering

Research paper thumbnail of Three-Dimensional Imaging by Confocal Scanning Fluorescence Microscopy

Research paper thumbnail of Confocal microscopy for the biological and material sciences: principle, applications, limitations

Proceedings of SPIE - The International Society for Optical Engineering

In the confocal scanning light microscope a specific volume is sampled during the imaging process... more In the confocal scanning light microscope a specific volume is sampled during the imaging process. The physical process is explained, together with how the size of the pinholes used affects the actual size of this volume. The thus produced 3-dimensional imaging is of high quality but subject to a number of limitations. A novel (bilateral scanning) arrangement is presented which may relieve some of these. Use is made in this approach of a double sided scanning mirror element and a charge coupled device (CCD) for image collection.

Research paper thumbnail of Confocal microscopy for the life sciences

Proceedings of SPIE - The International Society for Optical Engineering

In the confocal scanning light microscope a specific volume is sampled during the imaging process... more In the confocal scanning light microscope a specific volume is sampled during the imaging process. The physical process is explained, together with how the size of the pinholes used affect the actual size of this volume. The thus produced 3-D imaging is of high quality but subject to a number of limitations. A novel (bilateral scanning) arrangement is presented that may relieve some of these. In this approach, a double-sided scanning mirror element and a charge coupled device (CCD for image collection) are used.

Research paper thumbnail of Van Steensel B, van Binnendijk EP, Hornsby CD, van der Voort HT, Krozowski ZS, de Kloet ER et al. Partial colocalization of glucocorticoid and mineralocorticoid receptors in discrete compartments in nuclei of rat hippocampus neurons. J Cell Sci 109: 787-792

Journal of Cell Science

The glucocorticoid receptor and the mineralocorticoid receptor are hormone-dependent transcriptio... more The glucocorticoid receptor and the mineralocorticoid receptor are hormone-dependent transcription factors. They regulate the excitability of rat hippocampus CA1 neurons in a coordinated fashion. We studied the spatial distribution of these transcription factors in nuclei of CA1 neurons by dual labeling immunocytochemistry and confocal microscopy, combined with novel image restoration and image analysis techniques. We found that both receptors are concentrated in about one thousand clusters within the nucleus. Some clusters contain either mineralocorticoid receptors or glucocorticoid receptors, but a significant number of clusters contains both receptors. These results indicate that the two receptor types are targeted to specific compartments in the nucleus. The coordinated action of the glucocorticoid and mineralocorticoid receptor on gene expression may be established in a specific set of nuclear domains that contain both receptors.

Research paper thumbnail of A 3‐D model for chromatin organisation of G1 and G2 populations from quantitative confocal image analysis

Cytometry, 1997

A study on the chromatin organisation of synchronised G1 and G2 populations of maize root cell nu... more A study on the chromatin organisation of synchronised G1 and G2 populations of maize root cell nuclei is reported using 3-D images acquired with a confocal fluorescence microscope. The analysis is based on the concept of accessibility. Accessibility of a position x is the effort to arrive at x, when choosing the minimum effort path to arrive at x from the nuclear border. The effort is then taken to be proportional to the amount of all mass encountered on the path, and computed by a technique called the grey valued distance transform. The approach relies heavily on quantitative analysis of the intensity information. Hence, considerable attention was paid to the quantitative modification of the confocal intensity values by diffraction, absorption and scatter corrections. Three texture features are extracted from the accessibility maps: the global object inaccessibility, the relative object accessibility, and the object homogeneity. On the basis of individual texture features, no distinction between the G1 and G2 populations could be established. However, the three features combined did show a clear difference with a high significance.

Research paper thumbnail of Fast volume render techniques for interactive analysis

The Visual Computer, 1997

Without graphics hardware, interactive volume rendering is almost impossible with the current gen... more Without graphics hardware, interactive volume rendering is almost impossible with the current generation of computers and software. We describe the implementation of a volume renderer for interactive analysis of confocal images. We propose several techniques to accelerate the rendering of grey-value volumes. We propose to illuminate the volume selectively with ray templates to get a proper shadow cue in the shortest feasible time. In the viewing phase, rendering is distinctively accelerated for four user interactions: (1) a total change by successive adaptive refinement, (2) an unknown change in the view with this refinement strategy combined with suspended interpolation, (3) a known change in the view by recalculating only that part and (4) a view translation by recalculating the uncovered part.

Research paper thumbnail of A quantative comparison of two restoration methods as applied to confocal microscopy

Research paper thumbnail of A quantitative comparison of image restoration methods for confocal microscopy

Journal of Microscopy, 1997

Research paper thumbnail of Three-deimensional visualization of multi-channel volume data: The amSFP algorithm

Research paper thumbnail of Image analysis in biology Edited by Donat-P. Häder CRC Press, Boca Raton (1992) ISBN 0-8493-6033-1; 256 pages, illustrated, $179.00

Research paper thumbnail of Avalanche photodiode detection with object scanning and image restoration provides 2–4 fold resolution increase in two‐photon fluorescence microscopy

Bioimaging, 1996

ABSTRACT High-quantum-efficiency photodetection, millisecond pixel dwell time stage scanning and ... more ABSTRACT High-quantum-efficiency photodetection, millisecond pixel dwell time stage scanning and image restoration by maximum-likelihood estimation are synergetically combined and shown to improve the resolution of two-photon excitation microscopy 2-4 fold in all directions. Measurements of the two-photon excitation point-spread function (PSF) of a 1.4 aperture oil immersion lens are carried out by imaging fluorescence beads with a diameter of one seventh of the excitation wavelength (830 nm) and subsequent deconvolution with the bead object function. The proposed method of resolution increase is applied to beads as well as to rhodamine labelled actin fibres in mouse fibroblast cells. As the resolution improvement is not based on the non-linear effect of two-photon excitation, the results imply a comparable resolution increase in single-photon excitation confocal microscopy. In the fibroblasts, we established a three-fold improvement in axial resolution, namely from 840 nm before, to 280 nm after restoration (full-width at half-maximum). Actin fibres with axial distances of 850 nm, otherwise difficult to discern, are fully separated. In the lateral direction, images of fluorescence beads of about 110 nm diameter are restored to the real dimensions of the beads with an accuracy of better than one pixel (41 nm).

Research paper thumbnail of Spectral Volume Rendering

Ieee Transactions on Visualization and Computer Graphics, 2000

ÐVolume renderers for interactive analysis must be sufficiently versatile to render a broad range... more ÐVolume renderers for interactive analysis must be sufficiently versatile to render a broad range of volume images: unsegmented ªrawº images as recorded by a 3D scanner, labeled segmented images, multimodality images, or any combination of these. The usual strategy is to assign to each voxel a three component RGB color and an opacity value. This so-called RGB approach offers the possibility of distinguishing volume objects by color. However, these colors are connected to the objects themselves, thereby bypassing the idea that in reality the color of an object is also determined by the light source and light detectors c.q. human eyes. The physically realistic approach presented here models light interacting with the materials inside a voxel causing spectral changes in the light. The radiated spectrum falls upon a set of RGB detectors. The spectral approach is investigated to see whether it could enhance the visualization of volume data and interactive tools. For that purpose, a material is split into an absorbing part (the medium) and a scattering part (small particles). The medium is considered to be either achromatic or chromatic, while the particles are considered to scatter the light achromatically, elastically, or inelastically. It appears that inelastic scattering particles combined with an achromatic absorbing medium offer additional visual features: Objects are made visible through the surface structure of a surrounding volume object and volume and surface structures can be made visible at the same time. With one or two materials the method is faster than the RGB approach, with three materials the performance is equal. The spectral approach can be considered as an extension of the RGB approach with a greater visual flexibility and a better balance between quality and speed. Index TermsÐVolume rendering, light/matter interaction, light spectra, physical realism, visual cues.

Research paper thumbnail of Abstracts of the 2nd European Super-Resolution User-Club Meeting

The 2 nd meeting of the Leica Super-Resolution User Club was held from September 25 to 27, 2012 i... more The 2 nd meeting of the Leica Super-Resolution User Club was held from September 25 to 27, 2012 in collaboration with the Science for Life Laboratory at the Karolinska Institute, Stockholm, Sweden. With a mixture of engaging talks by key experts in the field of super-resolution microscopy and stimulating discussion sessions, the meeting proved as popular as last year's event, attracting a wide range of scientists interested in both confocal and widefield super-resolution and sample preparation techniques.

Research paper thumbnail of Quantitative 3-D texture analysis of interphase cell nuclei

Proceedings., 11th IAPR International Conference on Pattern Recognition. Vol. IV. Conference D: Architectures for Vision and Pattern Recognition,, 2000

Research paper thumbnail of Thee-dimensional visualization methods for confocal microscopy

Journal of Microscopy

ABSTRACT

Research paper thumbnail of Confocal Scanning Laser Fluorescence And Reflection Microscopy: Measurements Of The 3-D Image Formation And Applications In Biology

Research paper thumbnail of Dimensional imaging of biological structures by high resolution confocal microscopy. Scanning Microscopy, 2, 33

Scanning microscopy

ABSTRACT

Research paper thumbnail of Chapter 14 Three-Dimensional Confocal Fluorescence Microscopy

Research paper thumbnail of Three-dimensional arrangement of Crepis capillaris in mitotic prophase and anaphase as studied by confocal scanning laser microscopy

Journal of Cell Science

To estimate the extent of ordering of chromosomes, confocal scanning laser microscopy-was used to... more To estimate the extent of ordering of chromosomes, confocal scanning laser microscopy-was used to make three-dimensional images from optical sections. For Crepis capillaris, which has 2n = 6 easily recognizable chromosomes, a statistically significant sample of 75 Feulgen-stained root tip anaphases was analysed. A comparison of the observed chromosome ordering and the expected random distribution showed a significant surplus of one of the arrangements with a juxtaposition of the two chromosomes with a nucleolus organizer region. Two of the arrangements with these chromosomes in opposite positions were never observed in our material. Another analysis of 30 mithramycin Astained prophases and 30 meta-and anaphases showed partly different patterns of non-random chromosome distribution in the two stages of mitosis. A preference for an association of the homologues was observed for all pairs of chromosomes in prophase cells, whereas in meta-and anaphase the association only persisted for the nucleolus organizer chromosomes. This indicates that there may be some relocation of the chromosome positions during the transition from prophase to metaphase. In meta-and anaphase one of the arrangements with juxtaposed NOR chromosomes was preferred, i.e. the ordering in which chromosomes 1 and 3 occupied alternate positions. Probably, the nucleolus is an important factor in producing a non-random distribution, but there could be other factors that influence chromosome ordering as well. A comparison of the anaphase chromosome ordering in C. capillaris plants from very different localities, indicated that the observed non-random distribution was independent of the origin of the material. Existing models of chromosome disposition are not sufficient to explain the observed non-random chromosome ordering in C. capillaris.

Research paper thumbnail of Illumination and detection strategies for confocal microscopy

Proceedings of SPIE - The International Society for Optical Engineering

Research paper thumbnail of Three-Dimensional Imaging by Confocal Scanning Fluorescence Microscopy

Research paper thumbnail of Confocal microscopy for the biological and material sciences: principle, applications, limitations

Proceedings of SPIE - The International Society for Optical Engineering

In the confocal scanning light microscope a specific volume is sampled during the imaging process... more In the confocal scanning light microscope a specific volume is sampled during the imaging process. The physical process is explained, together with how the size of the pinholes used affects the actual size of this volume. The thus produced 3-dimensional imaging is of high quality but subject to a number of limitations. A novel (bilateral scanning) arrangement is presented which may relieve some of these. Use is made in this approach of a double sided scanning mirror element and a charge coupled device (CCD) for image collection.

Research paper thumbnail of Confocal microscopy for the life sciences

Proceedings of SPIE - The International Society for Optical Engineering

In the confocal scanning light microscope a specific volume is sampled during the imaging process... more In the confocal scanning light microscope a specific volume is sampled during the imaging process. The physical process is explained, together with how the size of the pinholes used affect the actual size of this volume. The thus produced 3-D imaging is of high quality but subject to a number of limitations. A novel (bilateral scanning) arrangement is presented that may relieve some of these. In this approach, a double-sided scanning mirror element and a charge coupled device (CCD for image collection) are used.

Research paper thumbnail of Van Steensel B, van Binnendijk EP, Hornsby CD, van der Voort HT, Krozowski ZS, de Kloet ER et al. Partial colocalization of glucocorticoid and mineralocorticoid receptors in discrete compartments in nuclei of rat hippocampus neurons. J Cell Sci 109: 787-792

Journal of Cell Science

The glucocorticoid receptor and the mineralocorticoid receptor are hormone-dependent transcriptio... more The glucocorticoid receptor and the mineralocorticoid receptor are hormone-dependent transcription factors. They regulate the excitability of rat hippocampus CA1 neurons in a coordinated fashion. We studied the spatial distribution of these transcription factors in nuclei of CA1 neurons by dual labeling immunocytochemistry and confocal microscopy, combined with novel image restoration and image analysis techniques. We found that both receptors are concentrated in about one thousand clusters within the nucleus. Some clusters contain either mineralocorticoid receptors or glucocorticoid receptors, but a significant number of clusters contains both receptors. These results indicate that the two receptor types are targeted to specific compartments in the nucleus. The coordinated action of the glucocorticoid and mineralocorticoid receptor on gene expression may be established in a specific set of nuclear domains that contain both receptors.