Biomedical subjects

L J van Vliet

Publications and source records attributed to L J van Vliet.

10 recordsLinked to original sources

PubMed2006

Shaving diffusion tensor images in discriminant analysis: a study into schizophrenia.

A technique called 'shaving' is introduced to automatically extract the combination of relevant image regions in a comparative study. No hypothesis is needed, as in conventional pre-defined or expert selected region of interest (ROI)-analysis. In contrast to traditional voxel based analysis (VBA), correlations within the data can be modeled using principal component analysis (PCA) and linear discriminant analysis (LDA). A study into schizophrenia using diffusion tensor imaging (DTI) serves as an application. Conventional VBA found a decreased fractional anisotropy (FA) in a part of the genu of the corpus callosum and an increased FA in larger parts of white matter. The proposed method reproduced the decrease in FA in the corpus callosum and found an increase in the posterior limb of the internal capsule and uncinate fasciculus. A correlation between the decrease in the corpus callosum and the increase in the uncinate fasciculus was demonstrated.

Adolescent↗

PubMed2005

Segmentation and size measurement of polyps in CT colonography.

Virtual colonoscopy is a relatively new method for the detection of colonic polyps. Their size, which is measured from reformatted CT images, mainly determines diagnosis. We present an automatic method for measuring the polyp size. The method is based on a robust segmentation method that grows a surface patch over the entire polyp surface starting from a seed. Projection of the patch points along the polyp axis yields a 2D point set to which we fit an ellipse. The long axis of the ellipse denotes the size of the polyp. We evaluate our method by comparing the automated size measurement with those of two radiologists using scans of a colon phantom. We give data for inter-observer and intra-observer variability of radiologists and our method as well as the accuracy and precision.

Algorithms↗

PubMed2005

Using line segments as structuring elements for sampling-invariant measurements.

When performing measurements in digitized images, the pixel pitch does not necessarily limit the attainable accuracy. Proper sampling of a band-limited continuous-domain image preserves all information present in the image prior to digitization. It is therefore (theoretically) possible to obtain measurements from the digitized image that are identical to measurements made in the continuous domain. Such measurements are sampling invariant, since they are independent of the chosen sampling grid. It is impossible to attain strict sampling invariance for filters in mathematical morphology due to their nonlinearity, but it is possible to approximate sampling invariance with arbitrary accuracy at the expense of additional computational cost. In this paper, we study morphological filters with line segments as structuring elements. We present a comparison of three known and three new methods to implement these filters. The method that yields a good compromise between accuracy and computational cost employs a (subpixel) skew to the image, followed by filtering along the grid axes using a discrete line segment, followed by an inverse skew. The staircase approximations to line segments under random orientations can be modeled by skewing a horizontal or vertical line segment. Rather than skewing the binary line segment we skew the image data, which substantially reduces quantization error. We proceed to determine the optimal number of orientations to use when measuring the length of line segments with unknown orientation.

Algorithms↗

PubMed2003

Ring formation in nanoliter cups: quantitative measurements of flow in micromachined wells.

Drying of DNA spots on microarrays and spilled coffee yields ringlike stains, because the outward flow transports dissolved particles to the border. Contact line pinning and diffusion limited evaporation of a liquid sample are the two necessary conditions to induce an outward directed liquid flow during evaporation. In this paper we present quantitative measurements of this flow field visualized by microspheres which are injected into a liquid sample in circular wells with a radius of 100-150 micro m and a depth of 6 micro m. The motion, including Brownian motion, of these microspheres with a radius of 0.25 micro m is recorded using digital fluorescence microscopy. Our analysis, using optic flow, does not require object identification, nor tracking of the individual objects. The spatiotemporal measurement space is sparsely filled at only those space/time positions where a microsphere is present. A confidence measure is computed indicating the presence of microspheres in this measurement space. The circular well shape allows us to transform the sparse measurement space into a denser, averaged radial velocity field. In this transformation we "interpolate" the radial velocity between values with a high confidence, which results in quantitative measurements of this outward flow field during the complete time interval of the evaporation process and at all radial positions in the circular wells. This allows for a quantitative validation of the elegant theory of ring formation.

Journal Article↗

PubMed2000

Mean and variance of ratio estimators used in fluorescence ratio imaging.

BACKGROUND: The ratio of two measured fluorescence signals (called x and y) is used in different applications in fluorescence microscopy. Multiple instances of both signals can be combined in different ways to construct different ratio estimators. METHODS: The mean and variance of three estimators for the ratio between two random variables, x and y, are discussed. Given n samples of x and y, we can intuitively construct two different estimators: the mean of the ratio of each x and y and the ratio between the mean of x and the mean of y. The former is biased and the latter is only asymptotically unbiased. Using the statistical characteristics of this estimator, a third, unbiased estimator can be constructed. RESULTS: We tested the three estimators on simulated data, real-world fluorescence test images, and comparative genome hybridization (CGH) data. The results on the simulated and real-world test images confirm the presented theory. The CGH experiments show that our new estimator performs better than the existing estimators. CONCLUSIONS: We have derived an unbiased ratio estimator that outperforms intuitive ratio estimators.

Analysis of Variance↗

PubMed2000

Background estimation in nonlinear image restoration.

One of the essential ways in which nonlinear image restoration algorithms differ from linear, convolution-type image restoration filters is their capability to restrict the restoration result to nonnegative intensities. The iterative constrained Tikhonov-Miller (ICTM) algorithm, for example, incorporates the nonnegativity constraint by clipping all negative values to zero after each iteration. This constraint will be effective only when the restored intensities have near-zero values. Therefore the background estimation will have an influence on the effectiveness of the nonnegativity constraint of these algorithms. We investigated quantitatively the dependency of the performance of the ICTM, Carrington, and Richardson-Lucy algorithms on the estimation of the background and compared it with the performance of the linear Tikhonov-Miller restoration filter. We found that the performance depends critically on the background estimation: An underestimation of the background will make the nonnegativity constraint ineffective, which results in a performance that does not differ much from the Tikhonov-Miller filter performance. A (small) overestimation, however, degrades the performance dramatically, since it results in a clipping of object intensities. We propose a novel general method to estimate the background based on the dependency of nonlinear restoration algorithms on the background, and we demonstrate its applicability on real confocal images.

Algorithms↗

PubMed1997

FISH and chips: automation of fluorescent dot counting in interphase cell nuclei.

Fluorescence in situ hybridization allows the enumeration of chromosomal abnormalities in interphase cell nuclei. This process is called dot counting. To estimate the distribution of chromosomes per cell, a large number of cells have to be analyzed, especially when the frequency of aberrant cells is low. Automation of dot counting is required because manual counting is tedious, fatiguing, and time-consuming. We developed a completely automated fluorescence microscope system that can examine 500 cells in approximately 15 min to determine the number of labeled chromosomes (seen as dots) in each cell nucleus. This system works with two fluorescent dyes, one for the DNA hybridization dots and one for the cell nucleus. After the stage has moved to a new field, the image is automatically focused, acquired by a Photometrics KAF 1400 camera (Photometrics Ltd., Tuscon, AZ, USA), and then analyzed on a Macintosh Quadra 840AV (Apple Computer, Inc., Cupertino, CA, USA) computer. After the required number of cells has been analyzed, the user may interact to correct the computer by working with a gallery of the cell images. The automated dot counter has been tested on a number of normal specimens where 4,'6-diamidino-2-phenylindole (DAPI) was used for the nucleus counterstain and a centromeric 8 probe was used to mark the desired chromosome. The slides contained lymphocytes from cultured blood. We compared the results of the dot counter with manual counting. Manually obtained results, published in the literature, were used as the "ground truth." For a normal specimen, 97.5% of cells will have two dots. Fully automated scanning of 13 slides showed that an average of 89% of all nuclei were counted correctly. In other words, an average of 11% has to be interactively corrected, using a monitor display. The machine accuracies, after interactive correction, are comparable to panels of human experts (manual). The fully automatically obtained results are biased with respect to manual counting. An error analysis is given, and different causes are discussed.

Algorithms↗

PubMed1997

Reconstruction of optical pathlength distributions from images obtained by a wide-field differential interference contrast microscope.

An image processing algorithm is presented to reconstruct optical pathlength distributions from images of nonabsorbing weak phase objects, obtained by a differential interference contrast (DIC) microscope, equipped with a charge-coupled device camera. The method is demonstrated on DIC images of transparent latex spheres and unstained bovine spermatozoa. The images were obtained with a wide-field DIC microscope, using monochromatic light. After image acquisition, the measured intensities were converted to pathlength differences. Filtering in the Fourier domain was applied to correct for the typical shadow-cast effect of DIC images. The filter was constructed using the lateral shift introduced in the microscope, and parameters describing the spectral distribution of the signal-to-noise ratio. By varying these parameters and looking at the resulting images, an appropriate setting for the filter parameters was found. In the reconstructed image each grey value represents the optical pathlength at that particular location, enabling quantitative analysis of object parameters using standard image processing techniques. The advantage of using interferometric techniques is that measurements can be done on transparent objects, without staining, enabling observations on living cells. Quantitative use of images obtained by a wide-field DIC microscope becomes possible with this technique, using relatively simple means.

Animals↗

PubMed1990

The Athena semi-automated karyotyping system.

In this article we describe Athena, a system that provides for semi-automated karyotyping of metaphase spreads. The system is based upon the Macintosh II computer. It uses software that is written entirely in C and consists of approximately 200 Kbytes of executable code. Athena provides automated segmentation of metaphase images into individual chromosomes, automated measurements on each banded chromosome, and automated classification into the standard Paris-convention karyotype. Furthermore, the system provides the ability to construct one or more chromosome data bases to represent the types of metaphase spreads and staining techniques that may be used in a given laboratory. Because we believe that it is impossible to construct a system that can achieve perfect segmentation, perfect separation of touching and overlapping chromosomes, perfect localization of the centromeres, and perfect classification, the system offers the possibility for interaction at each of the above stages using the well-accepted Macintosh user interface.

Centromere↗

PubMed1990

Experience with the Athena semi-automated karyotyping system.

The traditional analysis and assembly of metaphase chromosomes into a karyogram is a slow and tedious process requiring intermediate photographic steps and manual manipulation of the chromosome images. Much of this task is highly repetitive and readily lends itself to partial automation. Semi-automated karyotyping systems now are being used increasingly in both clinical and research cytogenetic laboratories. Digital image processing techniques are used to capture, manipulate, and make an initial classification of chromosome images. The Athena system uses commercially available components based on a Macintosh II personal computer. Digital image processing procedures automatically isolate chromosome images from the metaphase and arrange them into a karyogram, using information about relative chromosome length, centromeric index, and banding pattern. The operator uses the intuitive graphics interface of the Macintosh computer to monitor each phase of the analysis, to resolve any problems in isolating chromosome images, and to rearrange the individual chromosome images while assembling the final karyogram. Athena is designed as a semi-automated karyotyping system that is easy to learn and has sufficient power and versatility for routine use in the analysis of human metaphase chromosomes.

Humans↗