Luis Riazuelo

Pablo Azagra, Carlos Sostres, Ángel Ferrandez et al.

Computer-assisted systems are becoming broadly used in medicine. In endoscopy, most research focuses on the automatic detection of polyps or other pathologies, but localization and navigation of the endoscope are completely performed manually by physicians. To broaden this research and bring spatial Artificial Intelligence to endoscopies, data from complete procedures is needed. This paper introduces the Endomapper dataset, the first collection of complete endoscopy sequences acquired during regular medical practice, making secondary use of medical data. Its main purpose is to facilitate the development and evaluation of Visual Simultaneous Localization and Mapping (VSLAM) methods in real endoscopy data. The dataset contains more than 24 hours of video. It is the first endoscopic dataset that includes endoscope calibration as well as the original calibration videos. Meta-data and annotations associated with the dataset vary from the anatomical landmarks, procedure labeling, segmentations, reconstructions, simulated sequences with ground truth and same patient procedures. The software used in this paper is publicly available.

Clara Tomasini, Javier Rodriguez-Puigvert, Dinora Polanco et al.

Purpose: Subglottic stenosis refers to the narrowing of the subglottis, the airway between the vocal cords and the trachea. Its severity is typically evaluated by estimating the percentage of obstructed airway. This estimation can be obtained from CT data or through visual inspection by experts exploring the region. However, visual inspections are inherently subjective, leading to less consistent and robust diagnoses. No public methods or datasets are currently available for automated evaluation of this condition from bronchoscopy video. Methods: We propose a pipeline for automated subglottic stenosis severity estimation during the bronchoscopy exploration, without requiring the physician to traverse the stenosed region. Our approach exploits the physical effect of illumination decline in endoscopy to segment and track the lumen and obtain a 3D model of the airway. This 3D model is obtained from a single frame and is used to measure the airway narrowing. Results: Our pipeline is the first to enable automated and robust subglottic stenosis severity measurement using bronchoscopy images. The results show consistency with ground-truth estimations from CT scans and expert estimations, and reliable repeatability across multiple estimations on the same patient. Our evaluation is performed on our new Subglottic Stenosis Dataset of real bronchoscopy procedures data. Conclusion: We demonstrate how to automate evaluation of subglottic stenosis severity using only bronchoscopy. Our approach can assist with and shorten diagnosis and monitoring procedures, with automated and repeatable estimations and less exploration time, and save radiation exposure to patients as no CT is required. Additionally, we release the first public benchmark for subglottic stenosis severity assessment.

Clara Tomasini, Luis Riazuelo, Ana C. Murillo

Video bronchoscopy is a fundamental procedure in respiratory medicine, where medical experts navigate through the bronchial tree of a patient to diagnose or operate the patient. Surgeons need to determine the position of the scope as they go through the airway until they reach the area of interest. This task is very challenging for practitioners due to the complex bronchial tree structure and varying doctor experience and training. Navigation assistance to locate the bronchoscope during the procedure can improve its outcome. Currently used techniques for navigational guidance commonly rely on previous CT scans of the patient to obtain a 3D model of the airway, followed by tracking of the scope with additional sensors or image registration. These methods obtain accurate locations but imply additional setup, scans and training. Accurate metric localization is not always required, and a topological localization with regard to a generic airway model can often suffice to assist the surgeon with navigation. We present an image-based bronchoscopy topological localization pipeline to provide navigation assistance during the procedure, with no need of patient CT scan. Our approach is trained only on phantom data, eliminating the high cost of real data labeling, and presents good generalization capabilities. The results obtained surpass existing methods, particularly on real data test sequences.

Clara Tomasini, Luis Riazuelo, Ana C. Murillo

Automatic segmentation of anatomical landmarks in endoscopic images can provide assistance to doctors and surgeons for diagnosis, treatments or medical training. However, obtaining the annotations required to train commonly used supervised learning methods is a tedious and difficult task, in particular for real images. While ground truth annotations are easier to obtain for synthetic data, models trained on such data often do not generalize well to real data. Generative approaches can add realistic texture to it, but face difficulties to maintain the structure of the original scene. The main contribution in this work is a novel image translation model that adds realistic texture to simulated endoscopic images while keeping the key scene layout information. Our approach produces realistic images in different endoscopy scenarios. We demonstrate these images can effectively be used to successfully train a model for a challenging end task without any real labeled data. In particular, we demonstrate our approach for the task of fold segmentation in colonoscopy images. Folds are key anatomical landmarks that can occlude parts of the colon mucosa and possible polyps. Our approach generates realistic images maintaining the shape and location of the original folds, after the image-style-translation, better than existing methods. We run experiments both on a novel simulated dataset for fold segmentation, and real data from the EndoMapper (EM) dataset. All our new generated data and new EM metadata is being released to facilitate further research, as no public benchmark is currently available for the task of fold segmentation.

Inigo Alonso, Luis Riazuelo, Luis Montesano et al.

LiDAR semantic segmentation provides 3D semantic information about the environment, an essential cue for intelligent systems during their decision making processes. Deep neural networks are achieving state-of-the-art results on large public benchmarks on this task. Unfortunately, finding models that generalize well or adapt to additional domains, where data distribution is different, remains a major challenge. This work addresses the problem of unsupervised domain adaptation for LiDAR semantic segmentation models. Our approach combines novel ideas on top of the current state-of-the-art approaches and yields new state-of-the-art results. We propose simple but effective strategies to reduce the domain shift by aligning the data distribution on the input space. Besides, we propose a learning-based approach that aligns the distribution of the semantic classes of the target domain to the source domain. The presented ablation study shows how each part contributes to the final performance. Our strategy is shown to outperform previous approaches for domain adaptation with comparisons run on three different domains.

Iñigo Alonso, Luis Riazuelo, Luis Montesano et al.

LIDAR semantic segmentation, which assigns a semantic label to each 3D point measured by the LIDAR, is becoming an essential task for many robotic applications such as autonomous driving. Fast and efficient semantic segmentation methods are needed to match the strong computational and temporal restrictions of many of these real-world applications. This work presents 3D-MiniNet, a novel approach for LIDAR semantic segmentation that combines 3D and 2D learning layers. It first learns a 2D representation from the raw points through a novel projection which extracts local and global information from the 3D data. This representation is fed to an efficient 2D Fully Convolutional Neural Network (FCNN) that produces a 2D semantic segmentation. These 2D semantic labels are re-projected back to the 3D space and enhanced through a post-processing module. The main novelty in our strategy relies on the projection learning module. Our detailed ablation study shows how each component contributes to the final performance of 3D-MiniNet. We validate our approach on well known public benchmarks (SemanticKITTI and KITTI), where 3D-MiniNet gets state-of-the-art results while being faster and more parameter-efficient than previous methods.