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Juan Borrego-Carazo, Carles Sanchez, David Castells, Jordi Carrabina, & Debora Gil. (2023). BronchoPose: an analysis of data and model configuration for vision-based bronchoscopy pose estimation. CMPB - Computer Methods and Programs in Biomedicine, 228, 107241.
Abstract: Vision-based bronchoscopy (VB) models require the registration of the virtual lung model with the frames from the video bronchoscopy to provide effective guidance during the biopsy. The registration can be achieved by either tracking the position and orientation of the bronchoscopy camera or by calibrating its deviation from the pose (position and orientation) simulated in the virtual lung model. Recent advances in neural networks and temporal image processing have provided new opportunities for guided bronchoscopy. However, such progress has been hindered by the lack of comparative experimental conditions.
In the present paper, we share a novel synthetic dataset allowing for a fair comparison of methods. Moreover, this paper investigates several neural network architectures for the learning of temporal information at different levels of subject personalization. In order to improve orientation measurement, we also present a standardized comparison framework and a novel metric for camera orientation learning. Results on the dataset show that the proposed metric and architectures, as well as the standardized conditions, provide notable improvements to current state-of-the-art camera pose estimation in video bronchoscopy.
Keywords: Videobronchoscopy guiding; Deep learning; Architecture optimization; Datasets; Standardized evaluation framework; Pose estimation
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Sumit K. Banchhor, Narendra D. Londhe, Tadashi Araki, Luca Saba, Petia Radeva, Narendra N. Khanna, et al. (2018). Calcium detection, its quantification, and grayscale morphology-based risk stratification using machine learning in multimodality big data coronary and carotid scans: A review. CBM - Computers in Biology and Medicine, 101, 184–198.
Abstract: Purpose of review
Atherosclerosis is the leading cause of cardiovascular disease (CVD) and stroke. Typically, atherosclerotic calcium is found during the mature stage of the atherosclerosis disease. It is therefore often a challenge to identify and quantify the calcium. This is due to the presence of multiple components of plaque buildup in the arterial walls. The American College of Cardiology/American Heart Association guidelines point to the importance of calcium in the coronary and carotid arteries and further recommend its quantification for the prevention of heart disease. It is therefore essential to stratify the CVD risk of the patient into low- and high-risk bins.
Recent finding
Calcium formation in the artery walls is multifocal in nature with sizes at the micrometer level. Thus, its detection requires high-resolution imaging. Clinical experience has shown that even though optical coherence tomography offers better resolution, intravascular ultrasound still remains an important imaging modality for coronary wall imaging. For a computer-based analysis system to be complete, it must be scientifically and clinically validated. This study presents a state-of-the-art review (condensation of 152 publications after examining 200 articles) covering the methods for calcium detection and its quantification for coronary and carotid arteries, the pros and cons of these methods, and the risk stratification strategies. The review also presents different kinds of statistical models and gold standard solutions for the evaluation of software systems useful for calcium detection and quantification. Finally, the review concludes with a possible vision for designing the next-generation system for better clinical outcomes.
Keywords: Heart disease; Stroke; Atherosclerosis; Intravascular; Coronary; Carotid; Calcium; Morphology; Risk stratification
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Jorge Charco, Angel Sappa, Boris X. Vintimilla, & Henry Velesaca. (2021). Camera pose estimation in multi-view environments: From virtual scenarios to the real world. IVC - Image and Vision Computing, 110, 104182.
Abstract: This paper presents a domain adaptation strategy to efficiently train network architectures for estimating the relative camera pose in multi-view scenarios. The network architectures are fed by a pair of simultaneously acquired images, hence in order to improve the accuracy of the solutions, and due to the lack of large datasets with pairs of overlapped images, a domain adaptation strategy is proposed. The domain adaptation strategy consists on transferring the knowledge learned from synthetic images to real-world scenarios. For this, the networks are firstly trained using pairs of synthetic images, which are captured at the same time by a pair of cameras in a virtual environment; and then, the learned weights of the networks are transferred to the real-world case, where the networks are retrained with a few real images. Different virtual 3D scenarios are generated to evaluate the relationship between the accuracy on the result and the similarity between virtual and real scenarios—similarity on both geometry of the objects contained in the scene as well as relative pose between camera and objects in the scene. Experimental results and comparisons are provided showing that the accuracy of all the evaluated networks for estimating the camera pose improves when the proposed domain adaptation strategy is used, highlighting the importance on the similarity between virtual-real scenarios.
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Lei Kang, Pau Riba, Mauricio Villegas, Alicia Fornes, & Marçal Rusiñol. (2021). Candidate Fusion: Integrating Language Modelling into a Sequence-to-Sequence Handwritten Word Recognition Architecture. PR - Pattern Recognition, 112, 107790.
Abstract: Sequence-to-sequence models have recently become very popular for tackling
handwritten word recognition problems. However, how to effectively integrate an external language model into such recognizer is still a challenging
problem. The main challenge faced when training a language model is to
deal with the language model corpus which is usually different to the one
used for training the handwritten word recognition system. Thus, the bias
between both word corpora leads to incorrectness on the transcriptions, providing similar or even worse performances on the recognition task. In this
work, we introduce Candidate Fusion, a novel way to integrate an external
language model to a sequence-to-sequence architecture. Moreover, it provides suggestions from an external language knowledge, as a new input to
the sequence-to-sequence recognizer. Hence, Candidate Fusion provides two
improvements. On the one hand, the sequence-to-sequence recognizer has
the flexibility not only to combine the information from itself and the language model, but also to choose the importance of the information provided
by the language model. On the other hand, the external language model
has the ability to adapt itself to the training corpus and even learn the
most commonly errors produced from the recognizer. Finally, by conducting
comprehensive experiments, the Candidate Fusion proves to outperform the
state-of-the-art language models for handwritten word recognition tasks.
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G.Blasco, Simone Balocco, J.Puig, J.Sanchez-Gonzalez, W.Ricart, J.Daunis-I-Estadella, et al. (2015). Carotid pulse wave velocity by magnetic resonance imaging is increased in middle-aged subjects with the metabolic syndrome. ICJI - International Journal of Cardiovascular Imaging, 31(3), 603–612.
Abstract: Arterial pulse wave velocity (PWV), an independent predictor of cardiovascular disease, physiologically increases with age; however, growing evidence suggests metabolic syndrome (MetS) accelerates this increase. Magnetic resonance imaging (MRI) enables reliable noninvasive assessment of arterial stiffness by measuring arterial PWV in specific vascular segments. We investigated the association between the presence of MetS and its components with carotid PWV (cPWV) in asymptomatic subjects without diabetes. We assessed cPWV by MRI in 61 individuals (mean age, 55.3 ± 14.1 years; median age, 55 years): 30 with MetS and 31 controls with similar age, sex, body mass index, and LDL-cholesterol levels. The study population was dichotomized by the median age. To remove the physiological association between PWV and age, unpaired t tests and multiple regression analyses were performed using the residuals of the regression between PWV and age. cPWV was higher in middle-aged subjects with MetS than in those without (p = 0.001), but no differences were found in elder subjects (p = 0.313). cPWV was associated with diastolic blood pressure (r = 0.276, p = 0.033) and waist circumference (r = 0.268, p = 0.038). The presence of MetS was associated with increased cPWV regardless of age, sex, blood pressure, and waist (p = 0.007). The MetS components contributing independently to an increased cPWV were hypertension (p = 0.018) and hypertriglyceridemia (p = 0.002). The presence of MetS is associated with an increased cPWV in middle-aged subjects. In particular, hypertension and hypertriglyceridemia may contribute to early progression of carotid stiffness.
Keywords: Metabolic syndrome; Arterial stiffness; Pulse wave velocity; Carotid artery; Magnetic resonance
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Shiqi Yang, Yaxing Wang, Luis Herranz, Shangling Jui, & Joost Van de Weijer. (2023). Casting a BAIT for offline and online source-free domain adaptation. CVIU - Computer Vision and Image Understanding, 234, 103747.
Abstract: We address the source-free domain adaptation (SFDA) problem, where only the source model is available during adaptation to the target domain. We consider two settings: the offline setting where all target data can be visited multiple times (epochs) to arrive at a prediction for each target sample, and the online setting where the target data needs to be directly classified upon arrival. Inspired by diverse classifier based domain adaptation methods, in this paper we introduce a second classifier, but with another classifier head fixed. When adapting to the target domain, the additional classifier initialized from source classifier is expected to find misclassified features. Next, when updating the feature extractor, those features will be pushed towards the right side of the source decision boundary, thus achieving source-free domain adaptation. Experimental results show that the proposed method achieves competitive results for offline SFDA on several benchmark datasets compared with existing DA and SFDA methods, and our method surpasses by a large margin other SFDA methods under online source-free domain adaptation setting.
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Santiago Segui, Michal Drozdzal, Fernando Vilariño, Carolina Malagelada, Fernando Azpiroz, Petia Radeva, et al. (2012). Categorization and Segmentation of Intestinal Content Frames for Wireless Capsule Endoscopy. TITB - IEEE Transactions on Information Technology in Biomedicine, 16(6), 1341–1352.
Abstract: Wireless capsule endoscopy (WCE) is a device that allows the direct visualization of gastrointestinal tract with minimal discomfort for the patient, but at the price of a large amount of time for screening. In order to reduce this time, several works have proposed to automatically remove all the frames showing intestinal content. These methods label frames as {intestinal content – clear} without discriminating between types of content (with different physiological meaning) or the portion of image covered. In addition, since the presence of intestinal content has been identified as an indicator of intestinal motility, its accurate quantification can show a potential clinical relevance. In this paper, we present a method for the robust detection and segmentation of intestinal content in WCE images, together with its further discrimination between turbid liquid and bubbles. Our proposal is based on a twofold system. First, frames presenting intestinal content are detected by a support vector machine classifier using color and textural information. Second, intestinal content frames are segmented into {turbid, bubbles, and clear} regions. We show a detailed validation using a large dataset. Our system outperforms previous methods and, for the first time, discriminates between turbid from bubbles media.
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Jun Wan, Chi Lin, Longyin Wen, Yunan Li, Qiguang Miao, Sergio Escalera, et al. (2022). ChaLearn Looking at People: IsoGD and ConGD Large-scale RGB-D Gesture Recognition. TCIBERN - IEEE Transactions on Cybernetics, 52(5), 3422–3433.
Abstract: The ChaLearn large-scale gesture recognition challenge has been run twice in two workshops in conjunction with the International Conference on Pattern Recognition (ICPR) 2016 and International Conference on Computer Vision (ICCV) 2017, attracting more than 200 teams round the world. This challenge has two tracks, focusing on isolated and continuous gesture recognition, respectively. This paper describes the creation of both benchmark datasets and analyzes the advances in large-scale gesture recognition based on these two datasets. We discuss the challenges of collecting large-scale ground-truth annotations of gesture recognition, and provide a detailed analysis of the current state-of-the-art methods for large-scale isolated and continuous gesture recognition based on RGB-D video sequences. In addition to recognition rate and mean jaccard index (MJI) as evaluation metrics used in our previous challenges, we also introduce the corrected segmentation rate (CSR) metric to evaluate the performance of temporal segmentation for continuous gesture recognition. Furthermore, we propose a bidirectional long short-term memory (Bi-LSTM) baseline method, determining the video division points based on the skeleton points extracted by convolutional pose machine (CPM). Experiments demonstrate that the proposed Bi-LSTM outperforms the state-of-the-art methods with an absolute improvement of 8.1% (from 0.8917 to 0.9639) of CSR.
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Sergio Escalera, Vassilis Athitsos, & Isabelle Guyon. (2016). Challenges in multimodal gesture recognition. JMLR - Journal of Machine Learning Research, 17, 1–54.
Abstract: This paper surveys the state of the art on multimodal gesture recognition and introduces the JMLR special topic on gesture recognition 2011-2015. We began right at the start of the KinectTMrevolution when inexpensive infrared cameras providing image depth recordings became available. We published papers using this technology and other more conventional methods, including regular video cameras, to record data, thus providing a good overview of uses of machine learning and computer vision using multimodal data in this area of application. Notably, we organized a series of challenges and made available several datasets we recorded for that purpose, including tens of thousands
of videos, which are available to conduct further research. We also overview recent state of the art works on gesture recognition based on a proposed taxonomy for gesture recognition, discussing challenges and future lines of research.
Keywords: Gesture Recognition; Time Series Analysis; Multimodal Data Analysis; Computer Vision; Pattern Recognition; Wearable sensors; Infrared Cameras; KinectTM
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Xavier Carrillo, E Fernandez-Nofrerias, Francesco Ciompi, Oriol Rodriguez-Leor, Petia Radeva, Neus Salvatella, et al. (2011). Changes in Radial Artery Volume Assessed Using Intravascular Ultrasound: A Comparison of Two Vasodilator Regimens in Transradial Coronary Intervention. JOIC - Journal of Invasive Cardiology, 23(10), 401–404.
Abstract: OBJECTIVES:
This study used intravascular ultrasound (IVUS) to evaluate radial artery volume changes after intraarterial administration of nitroglycerin and/or verapamil.
BACKGROUND:
Radial artery spasm, which is associated with radial artery size, is the main limitation of the transradial approach in percutaneous coronary interventions (PCI).
METHODS:
This prospective, randomized study compared the effect of two intra-arterial vasodilator regimens on radial artery volume: 0.2 mg of nitroglycerin plus 2.5 mg of verapamil (Group 1; n = 15) versus 2.5 mg of verapamil alone (Group 2; n = 15). Radial artery lumen volume was assessed using IVUS at two time points: at baseline (5 minutes after sheath insertion) and post-vasodilator (1 minute after drug administration). The luminal volume of the radial artery was computed using ECOC Random Fields (ECOC-RF), a technique used for automatic segmentation of luminal borders in longitudinal cut images from IVUS sequences.
RESULTS:
There was a significant increase in arterial lumen volume in both groups, with an increase from 451 ± 177 mm³ to 508 ± 192 mm³ (p = 0.001) in Group 1 and from 456 ± 188 mm³ to 509 ± 170 mm³ (p = 0.001) in Group 2. There were no significant differences between the groups in terms of absolute volume increase (58 mm³ versus 53 mm³, respectively; p = 0.65) or in relative volume increase (14% versus 20%, respectively; p = 0.69).
CONCLUSIONS:
Administration of nitroglycerin plus verapamil or verapamil alone to the radial artery resulted in similar increases in arterial lumen volume according to ECOC-RF IVUS measurements.
Keywords: radial; vasodilator treatment; percutaneous coronary intervention; IVUS; volumetric IVUS analysis
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Diana Ramirez Cifuentes, Ana Freire, Ricardo Baeza Yates, Nadia Sanz Lamora, Aida Alvarez, Alexandre Gonzalez, et al. (2021). Characterization of Anorexia Nervosa on Social Media: Textual, Visual, Relational, Behavioral, and Demographical Analysis. JMIR - Journal of Medical Internet Research, 23(7), e25925.
Abstract: Background: Eating disorders are psychological conditions characterized by unhealthy eating habits. Anorexia nervosa (AN) is defined as the belief of being overweight despite being dangerously underweight. The psychological signs involve emotional and behavioral issues. There is evidence that signs and symptoms can manifest on social media, wherein both harmful and beneficial content is shared daily.
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Chengyi Zou, Shuai Wan, Tiannan Ji, Marc Gorriz Blanch, Marta Mrak, & Luis Herranz. (2023). Chroma Intra Prediction with Lightweight Attention-Based Neural Networks. TCSVT - IEEE Transactions on Circuits and Systems for Video Technology, 34(1), 549–560.
Abstract: Neural networks can be successfully used for cross-component prediction in video coding. In particular, attention-based architectures are suitable for chroma intra prediction using luma information because of their capability to model relations between difierent channels. However, the complexity of such methods is still very high and should be further reduced, especially for decoding. In this paper, a cost-effective attention-based neural network is designed for chroma intra prediction. Moreover, with the goal of further improving coding performance, a novel approach is introduced to utilize more boundary information effectively. In addition to improving prediction, a simplification methodology is also proposed to reduce inference complexity by simplifying convolutions. The proposed schemes are integrated into H.266/Versatile Video Coding (VVC) pipeline, and only one additional binary block-level syntax flag is introduced to indicate whether a given block makes use of the proposed method. Experimental results demonstrate that the proposed scheme achieves up to −0.46%/−2.29%/−2.17% BD-rate reduction on Y/Cb/Cr components, respectively, compared with H.266/VVC anchor. Reductions in the encoding and decoding complexity of up to 22% and 61%, respectively, are achieved by the proposed scheme with respect to the previous attention-based chroma intra prediction method while maintaining coding performance.
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Jordi Roca, C. Alejandro Parraga, & Maria Vanrell. (2013). Chromatic settings and the structural color constancy index. JV - Journal of Vision, 13(4-3), 1–26.
Abstract: Color constancy is usually measured by achromatic setting, asymmetric matching, or color naming paradigms, whose results are interpreted in terms of indexes and models that arguably do not capture the full complexity of the phenomenon. Here we propose a new paradigm, chromatic setting, which allows a more comprehensive characterization of color constancy through the measurement of multiple points in color space under immersive adaptation. We demonstrated its feasibility by assessing the consistency of subjects' responses over time. The paradigm was applied to two-dimensional (2-D) Mondrian stimuli under three different illuminants, and the results were used to fit a set of linear color constancy models. The use of multiple colors improved the precision of more complex linear models compared to the popular diagonal model computed from gray. Our results show that a diagonal plus translation matrix that models mechanisms other than cone gain might be best suited to explain the phenomenon. Additionally, we calculated a number of color constancy indices for several points in color space, and our results suggest that interrelations among colors are not as uniform as previously believed. To account for this variability, we developed a new structural color constancy index that takes into account the magnitude and orientation of the chromatic shift in addition to the interrelations among colors and memory effects.
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Ivan Huerta, Michael Holte, Thomas B. Moeslund, & Jordi Gonzalez. (2015). Chromatic shadow detection and tracking for moving foreground segmentation. IMAVIS - Image and Vision Computing, 41, 42–53.
Abstract: Advanced segmentation techniques in the surveillance domain deal with shadows to avoid distortions when detecting moving objects. Most approaches for shadow detection are still typically restricted to penumbra shadows and cannot cope well with umbra shadows. Consequently, umbra shadow regions are usually detected as part of moving objects, thus a ecting the performance of the nal detection. In this paper we address the detection of both penumbra and umbra shadow regions. First, a novel bottom-up approach is presented based on gradient and colour models, which successfully discriminates between chromatic moving cast shadow regions and those regions detected as moving objects. In essence, those regions corresponding to potential shadows are detected based on edge partitioning and colour statistics. Subsequently (i) temporal similarities between textures and (ii) spatial similarities between chrominance angle and brightness distortions are analysed for each potential shadow region for detecting the umbra shadow regions. Our second contribution re nes even further the segmentation results: a tracking-based top-down approach increases the performance of our bottom-up chromatic shadow detection algorithm by properly correcting non-detected shadows.
To do so, a combination of motion lters in a data association framework exploits the temporal consistency between objects and shadows to increase
the shadow detection rate. Experimental results exceed current state-of-the-
art in shadow accuracy for multiple well-known surveillance image databases which contain di erent shadowed materials and illumination conditions.
Keywords: Detecting moving objects; Chromatic shadow detection; Temporal local gradient; Spatial and Temporal brightness and angle distortions; Shadow tracking
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Mireia Sole, Joan Blanco, Debora Gil, Oliver Valero, Alvaro Pascual, B. Cardenas, et al. (2021). Chromosomal positioning in spermatogenic cells is influenced by chromosomal factors associated with gene activity, bouquet formation, and meiotic sex-chromosome inactivation. Chromosoma, 130, 163–175.
Abstract: Chromosome territoriality is not random along the cell cycle and it is mainly governed by intrinsic chromosome factors and gene expression patterns. Conversely, very few studies have explored the factors that determine chromosome territoriality and its influencing factors during meiosis. In this study, we analysed chromosome positioning in murine spermatogenic cells using three-dimensionally fluorescence in situ hybridization-based methodology, which allows the analysis of the entire karyotype. The main objective of the study was to decipher chromosome positioning in a radial axis (all analysed germ-cell nuclei) and longitudinal axis (only spermatozoa) and to identify the chromosomal factors that regulate such an arrangement. Results demonstrated that the radial positioning of chromosomes during spermatogenesis was cell-type specific and influenced by chromosomal factors associated to gene activity. Chromosomes with specific features that enhance transcription (high GC content, high gene density and high numbers of predicted expressed genes) were preferentially observed in the inner part of the nucleus in virtually all cell types. Moreover, the position of the sex chromosomes was influenced by their transcriptional status, from the periphery of the nucleus when its activity was repressed (pachytene) to a more internal position when it is partially activated (spermatid). At pachytene, chromosome positioning was also influenced by chromosome size due to the bouquet formation. Longitudinal chromosome positioning in the sperm nucleus was not random either, suggesting the importance of ordered longitudinal positioning for the release and activation of the paternal genome after fertilisation.
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