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PubMed2004

CT colonography with computer-aided detection: automated recognition of ileocecal valve to reduce number of false-positive detections.

The ileocecal valve (ICV) is a common cause of false-positive detections of polyps at computed tomographic (CT) colonography with computer-aided detection (CAD). The authors developed a CAD algorithm for differentiating the ICV from a true polyp and evaluated this algorithm by using two colonoscopy-confirmed CT colonography data sets. Data sets 1 and 2 consisted of the data obtained at CT colonographic examinations performed in 20 and 40 patients, respectively. Forty of these patients had at least one polyp 1 cm or larger. For data set 1, the proposed ICV recognition algorithm eliminated three of nine (33%; 95% confidence interval [CI]: 8%, 70%) false-positive CAD detections that were attributable to the ICV and none of the true-positive polyp detections. For data set 2, with use of identical parameters, the algorithm eliminated 11 of 18 (61%; 95% CI: 36%, 83%) false-positive detections that were attributable to the ICV and none of the true-positive detections. The thresholds used to recognize the ICV were a mean internal CT attenuation of less than -124 HU and a volume of greater than 1.5 cm(3). The proposed algorithm successfully recognized the ICV and eliminated it in some cases. This result is clinically important because, by reducing the frequency of a common cause of false-positive detections, this algorithm may improve the efficiency of physicians who use CAD.

Adult↗
PubMed2006

Automated on-the-fly detection and correction procedure for EPR imaging data acquisition.

Fast and reliable data acquisition is a major requirement for successful and useful biological electron paramagnetic resonance imaging (EPRI) experiments. Even a technologically advanced and professionally supervised EPRI system can exhibit instabilities initiated by perturbations such as animal motion, microphonics, and temperature changes. As a result, part of an acquired data set may become corrupted with excessive noise and distortions, which in turn may degrade the quality of the reconstructed image. In this work an automated scheme to monitor the system performance and stability over the course of an experiment is demonstrated. This method ensures that the quality of the acquired data is maintained during the experiment. For this purpose, four parameters including noise content and integration of each acquired projection are quantified and measured against those of the zero-gradient (ZG) projection, which is set as a quality benchmark. Projections with parameter values that differ substantially from the expected values are identified as damaged and consequently are reacquired. Therefore, the proposed technique not only effectively monitors the quality of acquisition, it also saves a substantial amount of acquisition time because it eliminates the necessity of repeating the entire experiment in cases in which only a small fraction of the data are corrupted.

Algorithms↗
PubMed2006

Smooth surface meshing for automated finite element model generation from 3D image data.

Finite element (FE) modelling based on data from three-dimensional high-resolution computed tomography (CT) imaging systems provides a non-invasive method to assess structural mechanics. Automated mesh generation from these voxel based image data can be achieved by direct conversion to hexahedron elements, however these model representations have jagged edges. This paper proposes an automated method to generate smoothed FE meshes from voxel-based image data. Mesh fairing processes are utilized that allow constraints that control the smoothing process, and are computationally efficient. Surfaces of the mesh on the exterior, as well as interfaces between two tissues, can be smoothed by varying fairing parameters and constraint criteria. The method was tested on a variety of real and simulated three-dimensional data sets, resulting in both hexahedron and tetrahedron meshes. It was shown that the fairing process is linearly related to the number of smoothing iterations, and that peak stresses are reduced in FE simulations of the smoothed models. Although developed for micro-CT data sets, this fast and reliable mesh smoothing method could be applied to any three-dimensional image data where node and element connectivity have been defined.

Animals↗
PubMed1979

Detection of suspicious cells and rejection of artefacts in cervical cytology using the Leyden Television Analysis System.

In slide based automation of cervical cytology the first stage of analysis involves finding possibly suspicious cells, or areas on the slide with these types of cells. By using a television based system such as the Leyden Television Analysis System (LEYTAS), a number of detection methods can be applied to rapidly screen a large number of fields automatically for suspicious cells. In this paper, results using a parameter based on increased nuclear DNA content of cells are given and a second detection method based on a chromatin pattern feature, called chromatin contrast, is discussed. Two blind trials on 41 positive and 22 negative cervical slides, using the Leyden Television Analysis System to detect suspicious cells with an increased nuclear DNA content, were promising. In 1 of the 41 positive cases no suspicious cells were found. In the negative specimens, suspicious cells were detected in 1 of 9 cases and 1 of 13 cases, with the two detection parameters investigated. These findings are discussed and some automatic artefact rejection procedures with preliminary results are given.

Cervix Uteri↗
PubMed2005

Automated validation of polymerase chain reactions using amplicon melting curves.

PCR, the polymerase chain reaction, is a fundamental tool of molecular biology. Quantitative PCR is the gold-standard methodology for determination of DNA copy numbers, quantitating transcription, and numerous other applications. A major barrier to large-scale application of PCR for quantitative genomic analyses is the current requirement for manual validation of individual PCR reactions to ensure generation of a single product. This typically requires visual inspection either of gel electrophoreses or temperature dissociation ("melting") curves of individual PCR reactions - a time-consuming and costly process. Here we describe a robust computational solution to this fundamental problem. Using a training set of 10,080 reactions comprising multiple quantitative PCR reactions from each of 1,728 unique human genomic amplicons, we developed a support vector machine classifier capable of discriminating single-product PCR reactions with better than 99% accuracy. This approach has broad utility, and eliminates a major bottleneck to widespread application of PCR for high-throughput genomic applications.

Algorithms↗
PubMed2003

An adjustable-threshold algorithm for the identification of objects in three-dimensional images.

MOTIVATION: To develop a highly accurate, practical and fast automated segmentation algorithm for three-dimensional images containing biological objects. To test the algorithm on images of the Drosophila brain, and identify, count and determine the locations of neurons in the images. RESULTS: A new adjustable-threshold algorithm was developed to efficiently segment fluorescently labeled objects contained within three-dimensional images obtained from laser scanning confocal microscopy, or two-photon microscopy. The result of the test segmentation with Drosophila brain images showed that the algorithm is extremely accurate and provided detailed information about the locations of neurons in the Drosophila brain. Centroids of each object (nucleus of each neuron) were also recorded into an algebraic matrix that describes the locations of the neurons. AVAILABILITY: Interested parties should send their request for the NeuronMapper(TM) program with the segmentation algorithm to artemp@bcm.tmc.edu.

Algorithms↗
PubMed2004

Detection of lumen-intima interface of posterior wall for measurement of elasticity of the human carotid artery.

In our series of studies on noninvasive assessment of the regional elasticity of the arterial wall, the displacement gradient (change in thickness) of the arterial wall caused by the heartbeat was measured by the phased-tracking method. Because the displacement gradient corresponds to the strain due to the change in blood pressure, the elasticity can be evaluated from the displacement gradient of the arterial wall and the blood pressure, which are noninvasively measured at the upper arm. In the measurement of the elasticity of the arterial wall by our method, the region in which the elastic modulus is estimated must be assigned beforehand; currently, the lumen-intima boundary of the arterial wall is manually determined by the operator. For the real-time measurement of the elasticity of the arterial wall, a fast, automated method is necessary for detection of the boundary. In this paper, a cost function is proposed for differentiation of the arterial wall from the lumen. The proposed cost function was applied to ultrasound data, which were noninvasively obtained for five human carotid arteries. In comparison with the case of detection using only the amplitude of the echo, the root mean square error between the automatically detected lumen-intima boundary and the manually assigned boundary was significantly improved by using the proposed cost function. Furthermore, the lumen-intima boundary was automatically detected in a short period. Such a method is required for real-time measurement of the elasticity of the arterial wall, though detection of the outer boundary of the adventitia, which is not described in this paper, is also necessary to realize real-time elasticity measurement by our method.

Adult↗
PubMed2003

An automated method for the detection of pulmonary embolism in V/Q-scans.

In this paper, a fully automatic method for the diagnosis of pulmonary embolism (PE) from V/Q-scans is presented. Image analysis is applied to the ventilation and the perfusion images obtained in the V/Q-scan. The difference of the ventilation and the perfusion is calculated after transformation and hot-spot reduction of the images. From this difference image the integral of the underperfused areas are used as features. With the aid of these features a simple test for PE is devised. The method is evaluated on two sets of patients. One set comprises 102 patients who have undergone both V/Q-scanning and angiography. The performance given as the area under the Receiver Operating Characteristic (ROC) curve is 0.85. Another set is made up by the 507 consecutive patients examined with V/Q-scanning at Lund University Hospital in Sweden. In this case, the reference was the consensus opinion of two radiologists, the ROC-area is 0.67. A fully automatic and reasonably robust expert system is developed to aid the radiologist in the interpretation of V/Q-scans for PE.

Algorithms↗
PubMed2005

Automated extraction of temporal motor activity signals from video recordings of neonatal seizures based on adaptive block matching.

This paper presents an automated procedure developed to extract quantitative information from video recordings of neonatal seizures in the form of motor activity signals. This procedure relies on optical flow computation to select anatomical sites located on the infants' body parts. Motor activity signals are extracted by tracking selected anatomical sites during the seizure using adaptive block matching. A block of pixels is tracked throughout a sequence of frames by searching for the most similar block of pixels in subsequent frames; this search is facilitated by employing various update strategies to account for the changing appearance of the block. The proposed procedure is used to extract temporal motor activity signals from video recordings of neonatal seizures and other events not associated with seizures.

Algorithms↗
PubMed2006

Quantitative assessment of breast density from digitized mammograms into Tabar's patterns.

We describe a semi-automated technique for the quantitative assessment of breast density from digitized mammograms in comparison with patterns suggested by Tabar. It was developed using the MATLAB-based graphical user interface applications. It is based on an interactive thresholding method, after a short automated method that shows the fibroglandular tissue area, breast area and breast density each time new thresholds are placed on the image. The breast density is taken as a percentage of the fibroglandular tissue to the breast tissue areas. It was tested in four different ways, namely by examining: (i) correlation of the quantitative assessment results with subjective classification, (ii) classification performance using the quantitative assessment technique, (iii) interobserver agreement and (iv) intraobserver agreement. The results of the quantitative assessment correlated well (r2 = 0.92) with the subjective Tabar patterns classified by the radiologist (correctly classified 83% of digitized mammograms). The average kappa coefficient for the agreement between the readers was 0.63. This indicated moderate agreement between the three observers in classifying breast density using the quantitative assessment technique. The kappa coefficient of 0.75 for intraobserver agreement reflected good agreement between two sets of readings. The technique may be useful as a supplement to the radiologist's assessment in classifying mammograms into Tabar's pattern associated with breast cancer risk.

Absorptiometry, Photon↗
PubMed2005

Segmentation of thrombus in abdominal aortic aneurysms from CTA with nonparametric statistical grey level appearance modeling.

This paper presents a new method for deformable model-based segmentation of lumen and thrombus in abdominal aortic aneurysms from computed tomography (CT) angiography (CTA) scans. First the lumen is segmented based on two positions indicated by the user, and subsequently the resulting surface is used to initialize the automated thrombus segmentation method. For the lumen, the image-derived deformation term is based on a simple grey level model (two thresholds). For the more complex problem of thrombus segmentation, a grey level modeling approach with a nonparametric pattern classification technique is used, namely k-nearest neighbors. The intensity profile sampled along the surface normal is used as classification feature. Manual segmentations are used for training the classifier: samples are collected inside, outside, and at the given boundary positions. The deformation is steered by the most likely class corresponding to the intensity profile at each vertex on the surface. A parameter optimization study is conducted, followed by experiments to assess the overall segmentation quality and the robustness of results against variation in user input. Results obtained in a study of 17 patients show that the agreement with respect to manual segmentations is comparable to previous values reported in the literature, with considerable less user interaction.

Algorithms↗
PubMed2006

Unsupervised parameter optimization for automated retention time alignment of severely shifted gas chromatographic data using the piecewise alignment algorithm.

Simulated chromatographic separations were used to study the performance of piecewise retention time alignment and to demonstrate automated unsupervised (without a training set) parameter optimization. The average correlation coefficient between the target chromatogram and all remaining chromatograms in the data set was used to optimize the alignment parameters. This approach frees the user from providing class information and makes the alignment algorithm applicable to classifying completely unknown data sets. The average peak in the raw simulated data set was shifted up to two peak-widths-at-base (average relative shift=2.0) and after alignment the average relative shift was improved to 0.3. Piecewise alignment was applied to severely shifted GC separations of gasolines and reformate distillation fraction samples. The average relative shifts in the raw gasolines and reformates data were 4.7 and 1.5, respectively, but after alignment improved to 0.5 and 0.4, respectively. The effect of piecewise alignment on peak heights and peak areas is also reported. The average relative difference in peak height was -0.20%. The average absolute relative difference in area was 0.15%.

Algorithms↗
PubMed2006

Algorithms for automatic interpretation of high resolution mass spectra.

Automated interpretation of high-resolution mass spectra in a reliable and efficient manner represents a highly challenging computational problem. This work aims at developing methods for reducing a high-resolution mass spectrum into its monoisotopic peak list, and automatically assigning observed masses to known fragment ion masses if the protein sequence is available. The methods are compiled into a suite of data reduction algorithms which is called MasSPIKE (Mass Spectrum Interpretation and Kernel Extraction). MasSPIKE includes modules for modeling noise across the spectrum, isotopic cluster identification, charge state determination, separation of overlapping isotopic distributions, picking isotopic peaks, aligning experimental and theoretical isotopic distributions for estimating a monoisotopic peak's location, generating the monoisotopic mass list, and assigning the observed monoisotopic masses to possible protein fragments. The method is tested against a complex top-down spectrum of bovine carbonic anhydrase. Results of each of the individual modules are compared with previously published work.

Algorithms↗
PubMed2006

Strategies for adapting automated seizure detection algorithms.

The time-varying dynamics of epileptic seizures and the high inter-individual variability make their detection difficult. Osorio et al. [Osorio, I, Frei, MG, Wilkinson, SB. Real-time automated detection and quantitative analysis of seizures and short-term prediction of clinical onset. Epilepsia 1998;39(6):615-27] developed an algorithm that has had success in detecting seizures. We present a new strategy for adapting this algorithm or other algorithms to an individual's seizure fingerprint using both seizure and non-seizure training segments and a novel performance criterion that directly incorporates the non-linearity and lack of differentiability of the algorithm. The joint optimization of a linear filter chosen from a bank of candidate filters and of a percentile used in order statistic filtering provides an empirical solution that is both practical and useful, which should translate into improved sensitivity, specificity and detection speed. This premise is strongly supported by the results obtained in a large validation study and the examples illustrated in this article. This strategy is generalizable to other detection algorithms with modular architecture and spectral filters.

Algorithms↗
PubMed2004

Detection of skin cancer by classification of Raman spectra.

Skin lesion classification based on in vitro Raman spectroscopy is approached using a nonlinear neural network classifier. The classification framework is probabilistic and highly automated. The framework includes a feature extraction for Raman spectra and a fully adaptive and robust feedforward neural network classifier. Moreover, classification rules learned by the neural network may be extracted and evaluated for reproducibility, making it possible to explain the class assignment. The classification performance for the present data set, involving 222 cases and five lesion types, was 80.5%+/-5.3% correct classification of malignant melanoma, which is similar to that of trained dermatologists based on visual inspection. The skin cancer basal cell carcinoma has a classification rate of 95.8%+/-2.7%, which is excellent. The overall classification rate of skin lesions is 94.8%+/-3.0%. Spectral regions, which are important for network classification, are demonstrated to reproduce. Small distinctive bands in the spectrum, corresponding to specific lipids and proteins, are shown to hold the discriminating information which the network uses to diagnose skin lesions.

Artificial Intelligence↗
PubMed2005

A theoretical and experimental investigation of graph theoretical measures for land development in satellite imagery.

Today's commercial satellite images enable experts to classify region types in great detail. In previous work, we considered discriminating rural and urban regions [23]. However, a more detailed classification is required for many purposes. These fine classifications assist government agencies in many ways including urban planning, transportation management, and rescue operations. In a step toward the automation of the fine classification process, this paper explores graph theoretical measures over grayscale images. The graphs are constructed by assigning photometric straight line segments to vertices, while graph edges encode their spatial relationships. We then introduce a set of measures based on various properties of the graph. These measures are nearly monotonic (positively correlated) with increasing structure (organization) in the image. Thus, increased cultural activity and land development are indicated by increases in these measures-without explicit extraction of road networks, buildings, residences, etc. These latter, time consuming (and still only partially automated) tasks can be restricted only to "promising" image regions, according to our measures. In some applications our measures may suffice. We present a theoretical basis for the measures followed by extensive experimental results in which the measures are first compared to manual evaluations of land development. We then present and test a method to focus on, and (pre)extract, suburban-style residential areas. These are of particular importance in many applications, and are especially difficult to extract. In this work, we consider commercial IKONOS data. These images are orthorectified to provide a fixed resolution of 1 meter per pixel on the ground. They are, therefore, metric in the sense that ground distance is fixed in scale to pixel distance. Our data set is large and diverse, including sea and coastline, rural, forest, residential, industrial, and urban areas.

Algorithms↗
PubMed1995

An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching.

The generation of binding modes between two molecules, also known as molecular docking, is a key problem in rational drug design and biomolecular recognition. Docking a ligand, e.g., a drug molecule or a protein molecule, to a protein receptor, involves recognition of molecular surfaces as molecules interact at their surface. Recent studies report that the activity of many molecules induces conformational transitions by 'hinge-bending', which involves movements of relatively rigid parts with respect to each other. In ligand-receptor binding, relative rotational movements of molecular substructures about their common hinges have been observed. For automatically predicting flexible molecular interactions, we adapt a new technique developed in Computer Vision and Robotics for the efficient recognition of partially occluded articulated objects. These type of objects consist of rigid parts which are connected by rotary joints (hinges). Our approach is based on an extension and generalization of the Geometric Hashing and Generalized Hough Transform paradigm for rigid object recognition. Unlike other techniques which match each part individually, our approach exploits forcefully and efficiently enough the fact that the different rigid parts do belong to the same flexible molecule. We show experimental results obtained by an implementation of the algorithm for rigid and flexible docking. While the 'correct', crystal-bound complex is obtained with a small RMSD, additional, predictive 'high scoring' binding modes are generated as well. The diverse applications and implications of this general, powerful tool are discussed.

Algorithms↗
PubMed2002

Using a statistical shape model to extract sulcal curves on the outer cortex of the human brain.

A method for automated segmentation of major cortical sulci on the outer brain boundary is presented, with emphasis on automatically determining point correspondence and on labeling cortical regions. The method is formulated in a general optimization framework defined on the unit sphere, which serves as parametric domain for convoluted surfaces of spherical topology. A statistical shape model, which includes a network of deformable curves on the unit sphere, seeks geometric features such as high curvature regions and labels such features via a deformation process that is confined within a spherical map of the outer brain boundary. The limitations of the customary spherical coordinate system, which include discontinuities at the poles and nonuniform sampling, are overcome by defining the statistical prior of shape variation in terms of projections of landmark points onto corresponding tangent planes of the sphere. The method is tested against and shown to be as accurate as manually defined segmentations.

Algorithms↗