Jorge Márquez

Three-dimensional analysis of the arrangement of compact chromatin in the nucleus of G0 rat lymphocytes

The arrangement of compact chromatin of G0 lymphocytes was studied in three-dimensional reconstructions of the ensemble of the chromatin and of individual compact chromatin bodies. Rat spleen was serially cut and sections were contrasted with procedures preferential for DNA. Electron microscopy images were digitized, processed, and displayed using a commercial soft-ware package, complemented by a system for three-dimensional reconstruction and analysis developed by us on an IBM-compatible microcomputer provided with an image acquisition board. The reconstructions showed a continuous layer of compact chromatin in contact with the nuclear envelope that prevents the automatic recognition of individual chromatin clumps. The ensemble of the arrangement of compact chromatin was found to be very similar in different lymphocytes. After morphological filtering procedures, the initial mass was divided into individual bodies of compact chromatin, which were tagged. Most of these bodies contact the nuclear envelope. The number of bodies as well as the number of contacts with the envelope are similar and correspond to a haploid number of chromosomes. The largest body is always the one containing nucleolus-associated chromatin. When the cell has two nucleoli, the nucleolus-associated chromatin bodies contact the envelope in diametrically opposed areas. This feature was also described in rat liver cells. It is concluded that: (a) the individualized compact chromatin bodies do not correspond to an entire chromosome or to a pair of chromosomes; (b) the arrangement of compact chromatin is not identical in each G0 lymphocyte, but there are patterns that are repeated with limited changes; and (c) there are common features that appear in different cell types of individuals of the same species.

Pattern analysis of cell micronuclei images to evaluate their use as indicators of cell damage

Early biological changes that can be associated with disease are important indicators or biomarkers for the development of preventive screening strategies. Epidemiological studies have shown that the presence of chromosome damage or instability in human lymphocytes could be considered as an indicator of cancer risk. Chromosome damage can also be estimated using the micronuclei (MN) assay. MN are nuclear bodies originated by chromosome breakage or chromosome segregation during cell division. MN assay can be performed in epithelial tissues in direct contact with xenobiotics and carcinogens, becoming an indicator of cancer risk. Cell MN are thus geometric configurations that appear in the cell cytoplasm as small round bodies near the cell nucleus after cell division. Scoring micronuclei requires a trained individual to detect and count MN in approximately 3000-5000 cells from images in a microscope, becoming a tedious, subjective and error-prone task. In this paper we describe automated detection and counting techniques using digital image processing and pattern recognition, allowing automated detection and quantification of the cellular micronuclei configurations, making this technique much more effective for fast and reliable assessing of DNA damage by exposure to radiation and toxic substances.

Robust ellipsoidal model fitting of human heads

We report current work on methods for robust fitting of ellipsoids to the shape of the human head in three-dimensional models built from laser scanner acquisitions. A starting ellipsoid is obtained from Principal Component Analysis from mesh vertices; those regions far from the surface of the ellipsoid are penalized (outlier rejection and/or damping). A first method consists in re-calculating iteratively the ellipsoid by PCA, adjusting scales. Another method projects the outliers into the ellipsoid. A third method uses a morphological-error approach, via the difference of the distance fields of the head and its fitting ellipsoid. The ellipsoid orientation, position and scales are then changed in search for a set of parameters minimizing the morphological error. To speedup calculations, only a few orthogonal planes are sampled and the distance field is obtained directly from the triangular mesh elements. Among the intended applications, the restoration of the skullcap is presented.

Inter-chromosome texture as a feature for automatic identification of metaphase spreads

This paper reports results for a new measure of texture coarseness, as a step towards automation of metaphase finding in cell-proliferation studies. This measure is highly specific to grey-level inter-chromosome coarseness features in microscopic images of metaphase spreads and allows the texture quantification of cytological objects, analysing the intensity profile between chromosome-extrema samples. Chromosome fragments produce patterns of pixels at low resolution, and the local neighbourhood of their individual extrema presents a characteristic coarseness along intensity profiles, on randomly oriented test lines. Results of the use of this new measure on microscope images of fields of metaphases and artifacts are compared with some representative texture measures and the performance of reported metaphase finders. This new measure outperforms the latter, when applied in metaphase detection and elimination of artifacts. This coarseness feature provides a specific metaphase signature that can be used in conjunction with other morphological and textural parameters for automated metaphase discrimination.

Cartographic system for spatial distribution analysis of corneal endothelial cells

A combined cartographic and morphometric endothelium analyser has been developed by integrating the HISTO 2000 histological imaging and analysis system with a prototype human corneal endothelium analyser. The complete system allows the elaboration and analysis of cartographies of corneal endothelial tissue, and hence the in vitro study of the spatial distribution of corneal endothelial cells, according to their regional morphometric characteristics (cell size and polygonality). The global cartographic reconstruction is obtained by sequential integration of the data analysed for each microscopic field. Subsequently, the location of each microscopically analysed field is referred to its real position on the histologic preparation by means of X-Y co-ordinates; both are provided by micrometric optoelectronic sensors installed on the optical microscope stage. Some cartographies of an excised human corneal keratoconus button in vitro are also presented. These cartographic images allow a macroscopic view of endothelial cells analysed microscopically. Parametric colour images show the spatial distribution of endothelial cells, according to their specific morphometric parameters, and exhibit the variability in size and cellular shape which depend on the analysed area.

Low cost virtual face performance capture using stereo web cameras

A complete system for creating the performance of a virtual character is described. Stereo web-cameras perform marker based motion capture to obtain rigid head motion and non-rigid facial expression motion. Acquired 3D points are then mapped onto a 3D face model with a virtual muscle animation to create face expressions. Muscle inverse kinematics updates muscle contraction parameters based on marker motion to create the characters performance. Advantages of the system are reduced character creation time by using virtual muscles and a dynamic skin model, a novel way of applying markers to a face animation system, and its low cost hardware requirements, capable of running on standard hardware and making it suitable for interactive media in end-user environments.

Image-Fusion Operators for 3D Anatomical and Functional Analysis of the Brain

The goal of the present work is to obtain images combining in a useful and precise way the information present in 3D volumes of medical imaging sets. We address two modalities combining anatomy (Magnetic Resonance Imaging or MRI) and functional information (Positron Emission Tomography or PET). Commercial imaging software often offers image fusion tools based on fixed blending or color- channel combination of different modalities, and various popular color Look-Up Tables (LUTs), without considering the anatomical and functional character of the image features. We used a sensible approach for image fusion, taking advantage mainly from the HSL (Hue, Saturation and Luminosity) color space, in order to enhance the fusion results. We further tested operators for gradient and contour extraction to enhance anatomical details, such as feature borders, plus other spatial- domain filters for functional features, which correspond to wide point-spread-function responses in PET images. A set of image-fusion operators was formulated and tested on brain images from PET and MRI acquisitions.

Texture Analysis of Contrast-Enhanced Digital Mammography CEDM Images

A texture analysis aimed at finding correlations between textural descriptors and lesion diagnosis was applied to Contrast-Enhanced Digital Mammography CEDM subtracted images acquired under single-energy temporal subtraction modality using iodine-based contrast medium. The study, based on textural descriptors from Gray Level Co-occurrence Matrix GLCM, included 68 CEDM images of 17 patients, 10 cancer and 7 benign, acquired 1 to 5i¾?min after iodine injection. Seventeen GLCM descriptors were analyzed. Image processing consisted of geometric registration, logarithmic subtraction, and selection of regions-of-interest adipose, glandular and lesion ROIs by the radiologist. Results for lesion ROIs showed that homogeneity, normalized homogeneity, second-order inverse moment, energy and inverse variance were insensitive to the presence of iodine; a linear correlation existed between the sum mean and mean pixel value. Logistic regression showed that a linear combination of entropy and diagonal momentum discriminated between malignant and benign lesions with 79i¾?% specificity, 93i¾?% sensitivity and 87i¾?% accuracy.

Construction of a Model of the Upper Gastrointestinal System for the Simulation of Gastroesophagoendoscopic Procedures

We describe current work on the construction of three‐dimensional anatomical models of the upper gastrointestinal system, its computer navigation using a virtual endoscope, and the modeling of physical interactions of the model and the endoscope, including lens distortions and illumination conditions as well as collisions. This model will be part of a computer‐simulation system for the training of gastroendoscopic procedures.

Building a three-dimensional model of the upper gastrointestinal tract for computer simulations of swallowing

We aimed to provide realistic three-dimensional (3D) models to be used in numerical simulations of peristaltic flow in patients exhibiting difficulty in swallowing, also known as dysphagia. To this end, a 3D model of the upper gastrointestinal tract was built from the color cryosection images of the Visible Human Project dataset. Regional color heterogeneities were corrected by centering local histograms of the image difference between slices. A voxel-based model was generated by stacking contours from the color images. A triangle mesh was built, smoothed and simplified. Visualization tools were developed for browsing the model at different stages and for virtual endoscopy navigation. As result, a computer model of the esophagus and the stomach was obtained, mainly for modeling swallowing disorders. A central-axis curve was also obtained for virtual navigation and to replicate conditions relevant to swallowing disorders modeling. We show renderings of the model and discuss its use for simulating swallowing as a function of bolus rheological properties. The information obtained from simulation studies with our model could be useful for physicians in selecting the correct nutritional emulsions for patients with dysphagia.