Quantification of temporomandibular joint space in patients with juvenile idiopathic arthritis assessed by cone beam computerized tomography.

OBJECTIVE: To describe a method to calculate the total intra-articular volume (inter-osseous space) of the temporomandibular joint (TMJ) determined by cone-beam computed tomography (CBCT). This could be used as a marker of tissue proliferation and different degrees of soft tissue hyperplasia in juvenile idiopathic arthritis (JIA) patients. MATERIALS AND METHODS: Axial single-slice CBCT images of cross-sections of the TMJs of 11 JIA patients and 11 controls were employed. From the top of the glenoid fossa, in the caudal direction, an average of 26 slices were defined in each joint (N = 44). The interosseous space was manually delimited from each slice by using dedicated software that includes a graphic interface. TMJ volumes were calculated by adding the areas measured in each slice. Two volumes were defined: Ve-i and Vi , where Ve-i is the inter-osseous space, volume defined by the borders of the fossa and Vi is the internal volume defined by the condyle. An intra-articular volume filling index (IF) was defined as Ve-i /Vi , which represents the filling of the space. RESULTS: The measured space of the intra-articular volume, corresponding to the intra-articular soft tissue and synovial fluid, was more than twice as large in the JIA group as in the control group. CONCLUSION: The presented method, based on CBCT, is feasible for assessing inter-osseus joint volume of the TMJ and delimits a threshold of intra-articular changes related to intra-articular soft tissue proliferation, based on differences in volumes. Intra-articular soft tissue is found to be enlarged in JIA patients.

AutoMeKin2021: An open-source program for automated reaction discovery.

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.

Deep learning method for aortic root detection.

BACKGROUND: Computed tomography angiography (CTA) is a preferred imaging technique for a wide range of vascular diseases. However, extensive manual analysis is required to detect and identify several anatomical landmarks for clinical application. This study demonstrates the feasibility of a fully automatic method for detecting the aortic root, which is a key anatomical landmark in this type of procedure. The approach is based on the use of deep learning techniques that attempt to mimic expert behavior. METHODS: A total of 69 CTA scans (39 for training and 30 for validation) with different pathology types were selected to train the network. Furthermore, a total of 71 CTA scans were selected independently and applied as the test set to assess their performance. RESULTS: The accuracy was evaluated by comparing the locations marked by the method with benchmark locations (which were manually marked by two experts). The interobserver error was 4.6 ± 2.3 mm. On an average, the differences between the locations marked by the two experts and those detected by the computer were 6.6 ± 3.0 mm and 6.8 ± 3.3 mm, respectively, when calculated using the test set. CONCLUSIONS: From an analysis of these results, we can conclude that the proposed method based on pre-trained CNN models can accurately detect the aortic root in CTA images without prior segmentation.

Automatic detection of anatomical landmarks of the aorta in CTA images.

Computed tomography angiography (CTA) is one of the most common vascular imaging modalities. However, for clinical use, it still requires laborious manual analysis. This study demonstrates the feasibility of a fully automated technology for the accurate detection and identification of several anatomical reference points (landmarks), commonly used in intravascular imaging. This technology uses two different approaches, specially designed for the detection of aortic root and supra-aortic and visceral branches. In order to adjust the parameters of the developed algorithms, a total of 33 computed tomography scans with different types of pathologies were selected. Furthermore, a total of 30 independently selected computed tomography scans were used to assess their performance. Accuracy was evaluated by comparing the locations of reference points manually marked by human experts with those that were automatically detected. For supra-aortic and visceral branches detection, average values of 91.8 % for recall and 98.8 % for precision were obtained. For aortic root detection, the average difference between the positions marked by the experts and those detected by the computer was 5.7 ± 7.3 mm. Finally, diameters and lengths of the aorta were measured at different locations related to the extracted landmarks. Those measurements agreed with the values reported by the literature. Graphical abstract Schematic description of the proposed algorithm. The input includes an already segmented aorta (left), there are two main sub-processes related to the detection of branches and roots (center), and the output includes the segmented original aorta with the branches and the detected landmarks superimposed (right).

Noble microfluidic system for bioceramic nanoparticles engineering.

Bioceramic nanoparticles have many potential applications within the biomedical device industry. However, these applications demand a precise control of their sizes, shapes and morphology which play a main role in most properties. In this work, we report a new route for the synthesis of hydroxyapatite nanoparticles using a microfluidic device. The process is carried out by continuous laminar flow through the device. The obtained nanoparticles have showed same properties (composition, length, orientation, roughness) than those produced by conventional methods, however, our device can afford to fine tune the structure via simple engineering, i.e., produce nanoparticles of different size only by varying the flow velocity. In addition to the efficiency and novelty of this system, the optimization of personnel costs makes it very profitable economically.

Automatic estimation of the aortic lumen geometry by ellipse tracking.

PURPOSE: The shape and size of the aortic lumen can be associated with several aortic diseases. Automated computer segmentation can provide a mechanism for extracting the main features of the aorta that may be used as a diagnostic aid for physicians. This article presents a new fully automated algorithm to extract the aorta geometry for either normal (with and without contrast) or abnormal computed tomography (CT) cases. METHODS: The algorithm we propose is a fast incremental technique that computes the 3D geometry of the aortic lumen from an initial contour located inside it. Our approach is based on the optimization of the 3D orientation of the cross sections of the aorta. The method uses a robust ellipse estimation algorithm and an energy-based optimization technique to automatically track the centerline and the cross sections. The optimization involves the size and eccentricity of the ellipse which best fits the aorta contour on each cross-sectional plane. The method works directly on the original CT and does not require a prior segmentation of the aortic lumen. We present experimental results to show the accuracy of the method and its ability to cope with challenging CT cases where the aortic lumen may have low contrast, different kinds of pathologies, artifacts, and even significant angulations due to severe elongations. RESULTS: The algorithm correctly tracked the aorta geometry in 380 of 385 CT cases. The mean of the dice similarity coefficient was 0.951 for aorta cross sections that were randomly selected from the whole database. The mean distance to a manually delineated segmentation of the aortic lumen was 0.9 mm for sixteen selected cases. CONCLUSIONS: The results achieved after the evaluation demonstrate that the proposed algorithm is robust and accurate for the automatic extraction of the aorta geometry for both normal (with and without contrast) and abnormal CT volumes.

Categorical variables, interactions and generalized additive models. Applications in computer-aided diagnosis systems.

Recently, the generalized additive models (GAMs) have been presented as a novel statistical approach to distinguish lesion/non-lesion in computer-aided diagnosis (CAD) systems. In this paper, we present an extension of the GAM that allows for the introduction of factors and their interactions with continuous variables, for reducing false positives in a CAD system for detecting clustered microcalcifications in digital mammograms. The results obtained have shown an increase in the sensitivity from 83.12% to 85.71%, while the false positive rate was drastically reduced from 1.46 to 0.74 false detections per image.

Bootstrap-based procedures for inference in nonparametric receiver-operating characteristic curve regression analysis.

Prior to using a diagnostic test in a routine clinical setting, the rigorous evaluation of its diagnostic accuracy is essential. The receiver-operating characteristic curve is the measure of accuracy most widely used for continuous diagnostic tests. However, the possible impact of extra information about the patient (or even the environment) on diagnostic accuracy also needs to be assessed. In this paper, we focus on an estimator for the covariate-specific receiver-operating characteristic curve based on direct regression modelling and nonparametric smoothing techniques. This approach defines the class of generalised additive models for the receiver-operating characteristic curve. The main aim of the paper is to offer new inferential procedures for testing the effect of covariates on the conditional receiver-operating characteristic curve within the above-mentioned class. Specifically, two different bootstrap-based tests are suggested to check (a) the possible effect of continuous covariates on the receiver-operating characteristic curve and (b) the presence of factor-by-curve interaction terms. The validity of the proposed bootstrap-based procedures is supported by simulations. To facilitate the application of these new procedures in practice, an R-package, known as npROCRegression, is provided and briefly described. Finally, data derived from a computer-aided diagnostic system for the automatic detection of tumour masses in breast cancer is analysed.

Computerized detection of breast masses in digitized mammograms.

We propose a system to detect malignant masses on mammograms. We investigated the behavior of an iris filter at different scales. After iris filter was applied, suspicious regions were segmented by means of an adaptive threshold. Suspected regions were characterized with features based on the iris filter output and, gray level, texture, contour-related, and morphological features extracted from the image. A backpropagation neural network classifier was trained to reduce the number of false positives. The system was developed and evaluated with two completely independent data sets. Results for a test set of 66 malignant and 49 normal cases, evaluated with free-response receiver operating characteristic analysis, yielded a sensitivity of 88% and 94% at 1.02 false positives per image for lesion-based and case-based evaluation, respectively. Results suggest that the proposed method could help radiologists as a second reader in mammographic screening.

Using generalized additive models for construction of nonlinear classifiers in computer-aided diagnosis systems.

Several investigators have pointed out the possibility of using computer-aided diagnosis (CAD) schemes, as second readers, to help radiologists in the interpretation of images. One of the most important aspects to be considered when the diagnostic imaging systems are analyzed is the evaluation of their diagnostic performance. To perform this task, receiver operating characteristic curves are the method of choice. An important step in nearly all CAD systems is the reduction of false positives, as well as the classification of lesions, using different algorithms, such as neural networks or feature analysis, and several statistical methods. A statistical model more often employed is linear discriminant analysis (LDA). However, LDA implies several limitations in the type of variables that it can analyze. In this work, we have developed a novel approach, based on generalized additive models (GAMs), as an alternative to LDA, which can deal with a broad variety of variables, improving the results produced by using the LDA model. As an application, we have used GAM techniques for reducing the number of false detections in a computerized method to detect clustered microcalcifications, and we have compared this with the results obtained when LDA was applied. Employing LDA, the system achieved a sensitivity of 80.52% at a false-positive rate of 1.90 false detections per image. With the GAM, the sensitivity increased to 83.12% and 1.46 false positives per image.

Effects of JPEG2000 data compression on an automated system for detecting clustered microcalcifications in digital mammograms.

The functionalities of the JPEG2000 standard have led to its incorporation into digital imaging and communications in medicine (DICOM), which makes this compression method available for medical systems. In this study, we evaluated the compression of mammographic images with JPEG2000 (16 : 1, 20 : 1, 40 : 1, 60.4 : 1, 80: 1, and 106 : 1) for applications with a computer-aided detection (CAD) system for clusters of microcalcifications. Jackknife free-response receiver operating characteristic (JAFROC) analysis indicated that differences in the detection of clusters of microcalcifications were not statistically significant for uncompressed versus 16: 1 (T = -0.7780; p = 0.4370), 20 : 1 (T = 1.0361; p = 0.3007), and 40 : 1 (T = 1.6966; p = 0.0904); and statistically significant for uncompressed versus 60.4 : 1 (T = 5.8883; p < 0.008), 80 : 1 (T = 7.8414; p < 0.008), and 106 : 1 (T = 17.5034; p = < 0.008). Although there is a small difference in peak signal-to-noise ratio (PSNR) between compression ratios, the true-positive (TP) and false-positive (FP) rates, and the free-response receiver operating characteristic (FROC), figure of merit values considerably decreased from a 60 : 1 compression ratio. The performance of the CAD system is significantly reduced when using images compressed at ratios greater than 40 : 1 with JPEG2000 compared to uncompressed images. Mammographic images compressed up to 20 : 1 provide a percentage of correct detections by our CAD system similar to uncompressed images, regardless of the characteristics of the cluster. Further investigation is required to determine how JPEG2000 affects the detectability of clusters of microcalcifications as a function of their characteristics.

Automatic characterization of thoracic aortic aneurysms from CT images.

Accurate determination of the diameter is an important step for diagnosis and follow-up of aortic abnormalities such as aneurysms, caused by dilation of the vessel lumen. In this work we focus on the development of an automatic method for measuring the calibre of the thoracic aorta. The method is based on the application of principal component analysis on normal planes extracted from the aorta to establish the main axis of each section of the vessel. Two experiments were performed in order to test the accuracy and the rotational invariance of the developed method. Accuracy was determined by using a database of 15 clinical cases, where our method and a commercial software, which was considered as the gold standard, were compared. For the rotational invariance check, phantom images in different orientations were obtained and the diameter was measured with the proposed method. For clinical cases, a good agreement was observed between our method and the gold standard. The Bland Altman plots indicated that all of the values were within the acceptable limits of agreement with a bias of 0.2mm between both methods. For phantom cases, an ANOVA test revealed that the results achieved for the data sets acquired for the different orientations were not statistically different (F=1.88, p=0.153), which demonstrates the robustness of the method for rotations. The proposed method is applicable for measuring the diameter in all tested cases, and the results achieved underscored the capability of our approach for automatic characterization of thoracic aortic aneurysms.

Wavelet-based ultra-high compression of multidimensional NMR data sets.

The application of a lossy data compression algorithm based on wavelet transform to 2D NMR spectra is presented. We show that this algorithm affords rapid and extreme compression ratios (e.g., 800:1), providing high quality reconstructed 2D spectra. The algorithm was evaluated to ensure that qualitative and quantitative information are retained in the compressed NMR spectra. Whilst the maximum compression ratio that can be achieved depends on the number of signals and on the difference between the most and the least intense peaks (dynamic range), a compression ratio of 80:1 is affordable even for the challenging case of homonuclear 2D experiments of large biomolecules.

Region-based wavelet coding methods for digital mammography.

Spatial resolution and contrast sensitivity requirements for some types of medical image techniques, including mammography, delay the implementation of new digital technologies, namely, computer-aided diagnosis, picture archiving and communications systems, or teleradiology. In order to reduce transmission time and storage cost, an efficient data-compression scheme to reduce digital data without significant degradation of medical image quality is needed. In this study, we have applied two region-based compression methods to digital mammograms. In both methods, after segmenting the breast region, a region-based discrete wavelet transform is applied, followed by an object-based extension of the set partitioning in hierarchical trees (OB-SPIHT) coding algorithm in one method, and an object-based extension of the set partitioned embedded block (OB-SPECK) coding algorithm in the other. We have compared these specific implementations against the original SPIHT and the new standard JPEG 2000, both using reversible and irreversible filters, on five digital mammograms compressed at rates ranging from 0.1 to 1.0 bit per pixel (bbp). Distortion was evaluated for all images and compression rates by the peak signal-to-noise ratio. For all images, OB-SPIHT and OB-SPECK performed substantially better than the traditional SPIHT and JPEG 2000, and a slight difference in performance was found between them. A comparison applying SPIHT and the standard JPEG 2000 to the same set of images with the background pixels fixed to zero was also carried out, obtaining similar implementation as region-based methods. For digital mammography, region-based compression methods represent an improvement in compression efficiency from full-image methods, also providing the possibility of encoding multiple regions of interest independently.

Computer aided diagnosis for breast masses detection on a telemammography system.

A Computer-Aided Diagnosis (CAD) scheme for breast masses detection has been developed and integrated as a part of a telemammography system. This work derives from the close cooperation between the Laboratory for Radiologic Image Research of the University of Santiago de Compostela (Spain) and the company Intelsis Sistemas Inteligentes (Santiago de Compostela, Spain). This cooperation has been supported by funds from different projects, mainly from the European Union, the Spanish Health Administration, and the Galician Public Health's Service. As a result, a first prototype is ready to begin a demonstration project.

A high resolution workstation prototype for diagnosis of digital mammograms.

The development of a total digital high resolution mammography display system must meet a number of requirements that remain a challenge nowadays, most probably because of the special nature of breast imaging. In this paper, we discuss our particular approach to address some problems concerning the complexity of soft-copy diagnosis in digital mammography, such as image quality and user interface evaluation. Based on the experience obtained in the previous implementation of a medical image browser, a more ambitious project is being developed at the Department of Radiology of the University of Santiago de Compostela (Spain) in collaboration with the Department of Medical Informatics of INTELSIS, an emerging software company in our country. This new system will provide complete support to display, store and analyze mammographic studies in digital format.

A hybrid method based on level set and 3D region growing for segmentation of the thoracic aorta.

This study sought to develop a completely automatic method for image segmentation of the thoracic aorta. We used a total of 4682 images from 10 consecutive patients. The proposed method is based on the use of level set and region growing, automatically initialized using the Hough transform. The results obtained were compared to those of manual segmentation as performed by an external expert radiologist. Concordance between the developed method and manual segmentation ranged from 92.79 to 95.77% in the descending regions of the aorta and from 90.68 to 96.54% in the ascending regions, with a mean value of 93.83% being obtained for total segmentation.

Quantification of Right and Left Ventricular Function in Cardiac MR Imaging: Comparison of Semiautomatic and Manual Segmentation Algorithms.

The purpose of this study was to evaluate the performance of a semiautomatic segmentation method for the anatomical and functional assessment of both ventricles from cardiac cine magnetic resonance (MR) examinations, reducing user interaction to a "mouse-click". Fifty-two patients with cardiovascular diseases were examined using a 1.5-T MR imaging unit. Several parameters of both ventricles, such as end-diastolic volume (EDV), end-systolic volume (ESV) and ejection fraction (EF), were quantified by an experienced operator using the conventional method based on manually-defined contours, as the standard of reference; and a novel semiautomatic segmentation method based on edge detection, iterative thresholding and region growing techniques, for evaluation purposes. No statistically significant differences were found between the two measurement values obtained for each parameter (p > 0.05). Correlation to estimate right ventricular function was good (r > 0.8) and turned out to be excellent (r > 0.9) for the left ventricle (LV). Bland-Altman plots revealed acceptable limits of agreement between the two methods (95%). Our study findings indicate that the proposed technique allows a fast and accurate assessment of both ventricles. However, further improvements are needed to equal results achieved for the right ventricle (RV) using the conventional methodology.

Selecting variables in non-parametric regression models for binary response. An application to the computerized detection of breast cancer.

In many biomedical applications, interest lies in being able to distinguish between two possible states of a given response variable, depending on the values of certain continuous predictors. If the number of predictors, p, is high, or if there is redundancy among them, it then becomes important to decide on the selection of the best subset of predictors that will be able to obtain the models with greatest discrimination capacity. With this aim in mind, logistic generalized additive models were considered and receiver operating characteristic (ROC) curves were applied in order to determine and compare the discriminatory capacity of such models. This study sought to develop bootstrap-based tests that allow for the following to be ascertained: (a) the optimal number q < or = p of predictors; and (b) the model or models including q predictors, which display the largest AUC (area under the ROC curve). A simulation study was conducted to verify the behaviour of these tests. Finally, the proposed method was applied to a computer-aided diagnostic system dedicated to early detection of breast cancer.

Application of the iris filter for automatic detection of pulmonary nodules on computed tomography images.

We have developed a computer-aided diagnosis (CAD) system to detect pulmonary nodules on thin-slice helical computed tomography (CT) images. We have also investigated the capability of an iris filter to discriminate between nodules and false-positive findings. Suspicious regions were characterized with features based on the iris filter output, gray level and morphological features, extracted from the CT images. Functions calculated by linear discriminant analysis (LDA) were used to reduce the number of false-positives. The system was evaluated on CT scans containing 77 pulmonary nodules. The system was trained and evaluated using two completely independent data sets. Results for a test set, evaluated with free-response receiver operating characteristic (FROC) analysis, yielded a sensitivity of 80% at 7.7 false-positives per scan.