Yasin Almalioglu

Kutsev Bengisu Ozyoruk, Guliz Irem Gokceler, Gulfize Coskun et al.

Deep learning techniques hold promise to develop dense topography reconstruction and pose estimation methods for endoscopic videos. However, currently available datasets do not support effective quantitative benchmarking. In this paper, we introduce a comprehensive endoscopic SLAM dataset consisting of 3D point cloud data for six porcine organs, capsule and standard endoscopy recordings as well as synthetically generated data. A Panda robotic arm, two commercially available capsule endoscopes, two conventional endoscopes with different camera properties, and two high precision 3D scanners were employed to collect data from 8 ex-vivo porcine gastrointestinal (GI)-tract organs. In total, 35 sub-datasets are provided with 6D pose ground truth for the ex-vivo part: 18 sub-dataset for colon, 12 sub-datasets for stomach and 5 sub-datasets for small intestine, while four of these contain polyp-mimicking elevations carried out by an expert gastroenterologist. Synthetic capsule endoscopy frames from GI-tract with both depth and pose annotations are included to facilitate the study of simulation-to-real transfer learning algorithms. Additionally, we propound Endo-SfMLearner, an unsupervised monocular depth and pose estimation method that combines residual networks with spatial attention module in order to dictate the network to focus on distinguishable and highly textured tissue regions. The proposed approach makes use of a brightness-aware photometric loss to improve the robustness under fast frame-to-frame illumination changes. To exemplify the use-case of the EndoSLAM dataset, the performance of Endo-SfMLearner is extensively compared with the state-of-the-art. The codes and the link for the dataset are publicly available at https://github.com/CapsuleEndoscope/EndoSLAM. A video demonstrating the experimental setup and procedure is accessible through https://www.youtube.com/watch?v=G_LCe0aWWdQ.

Yasin Almalioglu, Kutsev Bengisu Ozyoruk, Abdulkadir Gokce et al.

Although wireless capsule endoscopy is the preferred modality for diagnosis and assessment of small bowel diseases, the poor camera resolution is a substantial limitation for both subjective and automated diagnostics. Enhanced-resolution endoscopy has shown to improve adenoma detection rate for conventional endoscopy and is likely to do the same for capsule endoscopy. In this work, we propose and quantitatively validate a novel framework to learn a mapping from low-to-high resolution endoscopic images. We combine conditional adversarial networks with a spatial attention block to improve the resolution by up to factors of 8x, 10x, 12x, respectively. Quantitative and qualitative studies performed demonstrate the superiority of EndoL2H over state-of-the-art deep super-resolution methods DBPN, RCAN and SRGAN. MOS tests performed by 30 gastroenterologists qualitatively assess and confirm the clinical relevance of the approach. EndoL2H is generally applicable to any endoscopic capsule system and has the potential to improve diagnosis and better harness computational approaches for polyp detection and characterization. Our code and trained models are available at https://github.com/CapsuleEndoscope/EndoL2H.

Yasin Almalioglu, Andrzej Kucik, Geoffrey French et al. · oxford

Object detection in satellite-borne Synthetic Aperture Radar (SAR) imagery holds immense potential in tasks such as urban monitoring and disaster response. However, the inherent complexities of SAR data and the scarcity of annotations present significant challenges in the advancement of object detection in this domain. Notably, the detection of small objects in satellite-borne SAR images poses a particularly intricate problem, because of the technology's relatively low spatial resolution and inherent noise. Furthermore, the lack of large labelled SAR datasets hinders the development of supervised deep learning-based object detection models. In this paper, we introduce TRANSAR, a novel self-supervised end-to-end vision transformer-based SAR object detection model that incorporates masked image pre-training on an unlabeled SAR image dataset that spans more than $25,700$ km\textsuperscript{2} ground area. Unlike traditional object detection formulation, our approach capitalises on auxiliary binary semantic segmentation, designed to segregate objects of interest during the post-tuning, especially the smaller ones, from the background. In addition, to address the innate class imbalance due to the disproportion of the object to the image size, we introduce an adaptive sampling scheduler that dynamically adjusts the target class distribution during training based on curriculum learning and model feedback. This approach allows us to outperform conventional supervised architecture such as DeepLabv3 or UNet, and state-of-the-art self-supervised learning-based arhitectures such as DPT, SegFormer or UperNet, as shown by extensive evaluations on benchmark SAR datasets.

Yasin Almalioglu, Angel Santamaria-Navarro, Benjamin Morrell et al.

In recent years, unsupervised deep learning approaches have received significant attention to estimate the depth and visual odometry (VO) from unlabelled monocular image sequences. However, their performance is limited in challenging environments due to perceptual degradation, occlusions and rapid motions. Moreover, the existing unsupervised methods suffer from the lack of scale-consistency constraints across frames, which causes that the VO estimators fail to provide persistent trajectories over long sequences. In this study, we propose an unsupervised monocular deep VO framework that predicts six-degrees-of-freedom pose camera motion and depth map of the scene from unlabelled RGB image sequences. We provide detailed quantitative and qualitative evaluations of the proposed framework on a) a challenging dataset collected during the DARPA Subterranean challenge; and b) the benchmark KITTI and Cityscapes datasets. The proposed approach outperforms both traditional and state-of-the-art unsupervised deep VO methods providing better results for both pose estimation and depth recovery. The presented approach is part of the solution used by the COSTAR team participating at the DARPA Subterranean Challenge.

Kagan Incetan, Ibrahim Omer Celik, Abdulhamid Obeid et al.

Current capsule endoscopes and next-generation robotic capsules for diagnosis and treatment of gastrointestinal diseases are complex cyber-physical platforms that must orchestrate complex software and hardware functions. The desired tasks for these systems include visual localization, depth estimation, 3D mapping, disease detection and segmentation, automated navigation, active control, path realization and optional therapeutic modules such as targeted drug delivery and biopsy sampling. Data-driven algorithms promise to enable many advanced functionalities for capsule endoscopes, but real-world data is challenging to obtain. Physically-realistic simulations providing synthetic data have emerged as a solution to the development of data-driven algorithms. In this work, we present a comprehensive simulation platform for capsule endoscopy operations and introduce VR-Caps, a virtual active capsule environment that simulates a range of normal and abnormal tissue conditions (e.g., inflated, dry, wet etc.) and varied organ types, capsule endoscope designs (e.g., mono, stereo, dual and 360°camera), and the type, number, strength, and placement of internal and external magnetic sources that enable active locomotion. VR-Caps makes it possible to both independently or jointly develop, optimize, and test medical imaging and analysis software for the current and next-generation endoscopic capsule systems. To validate this approach, we train state-of-the-art deep neural networks to accomplish various medical image analysis tasks using simulated data from VR-Caps and evaluate the performance of these models on real medical data. Results demonstrate the usefulness and effectiveness of the proposed virtual platform in developing algorithms that quantify fractional coverage, camera trajectory, 3D map reconstruction, and disease classification.

Chris Xiaoxuan Lu, Muhamad Risqi U. Saputra, Peijun Zhao et al.

Robust and accurate trajectory estimation of mobile agents such as people and robots is a key requirement for providing spatial awareness for emerging capabilities such as augmented reality or autonomous interaction. Although currently dominated by optical techniques e.g., visual-inertial odometry, these suffer from challenges with scene illumination or featureless surfaces. As an alternative, we propose milliEgo, a novel deep-learning approach to robust egomotion estimation which exploits the capabilities of low-cost mmWave radar. Although mmWave radar has a fundamental advantage over monocular cameras of being metric i.e., providing absolute scale or depth, current single chip solutions have limited and sparse imaging resolution, making existing point-cloud registration techniques brittle. We propose a new architecture that is optimized for solving this challenging pose transformation problem. Secondly, to robustly fuse mmWave pose estimates with additional sensors, e.g. inertial or visual sensors we introduce a mixed attention approach to deep fusion. Through extensive experiments, we demonstrate our proposed system is able to achieve 1.3% 3D error drift and generalizes well to unseen environments. We also show that the neural architecture can be made highly efficient and suitable for real-time embedded applications.

Yasin Almalioglu, Mehmet Turan, Alp Eren Sari et al.

In the last decade, numerous supervised deep learning approaches requiring large amounts of labeled data have been proposed for visual-inertial odometry (VIO) and depth map estimation. To overcome the data limitation, self-supervised learning has emerged as a promising alternative, exploiting constraints such as geometric and photometric consistency in the scene. In this study, we introduce a novel self-supervised deep learning-based VIO and depth map recovery approach (SelfVIO) using adversarial training and self-adaptive visual-inertial sensor fusion. SelfVIO learns to jointly estimate 6 degrees-of-freedom (6-DoF) ego-motion and a depth map of the scene from unlabeled monocular RGB image sequences and inertial measurement unit (IMU) readings. The proposed approach is able to perform VIO without the need for IMU intrinsic parameters and/or the extrinsic calibration between the IMU and the camera. estimation and single-view depth recovery network. We provide comprehensive quantitative and qualitative evaluations of the proposed framework comparing its performance with state-of-the-art VIO, VO, and visual simultaneous localization and mapping (VSLAM) approaches on the KITTI, EuRoC and Cityscapes datasets. Detailed comparisons prove that SelfVIO outperforms state-of-the-art VIO approaches in terms of pose estimation and depth recovery, making it a promising approach among existing methods in the literature.

Muhamad Risqi U. Saputra, Pedro P. B. de Gusmao, Chris Xiaoxuan Lu et al.

Visual odometry shows excellent performance in a wide range of environments. However, in visually-denied scenarios (e.g. heavy smoke or darkness), pose estimates degrade or even fail. Thermal cameras are commonly used for perception and inspection when the environment has low visibility. However, their use in odometry estimation is hampered by the lack of robust visual features. In part, this is as a result of the sensor measuring the ambient temperature profile rather than scene appearance and geometry. To overcome this issue, we propose a Deep Neural Network model for thermal-inertial odometry (DeepTIO) by incorporating a visual hallucination network to provide the thermal network with complementary information. The hallucination network is taught to predict fake visual features from thermal images by using Huber loss. We also employ selective fusion to attentively fuse the features from three different modalities, i.e thermal, hallucination, and inertial features. Extensive experiments are performed in hand-held and mobile robot data in benign and smoke-filled environments, showing the efficacy of the proposed model.

Yasin Almalioglu, Mehmet Turan, Chris Xiaoxuan Lu et al.

Robust indoor ego-motion estimation has attracted significant interest in the last decades due to the fast-growing demand for location-based services in indoor environments. Among various solutions, frequency-modulated continuous-wave (FMCW) radar sensors in millimeter-wave (MMWave) spectrum are gaining more prominence due to their intrinsic advantages such as penetration capability and high accuracy. Single-chip low-cost MMWave radar as an emerging technology provides an alternative and complementary solution for robust ego-motion estimation, making it feasible in resource-constrained platforms thanks to low-power consumption and easy system integration. In this paper, we introduce Milli-RIO, an MMWave radar-based solution making use of a single-chip low-cost radar and inertial measurement unit sensor to estimate six-degrees-of-freedom ego-motion of a moving radar. Detailed quantitative and qualitative evaluations prove that the proposed method achieves precisions on the order of few centimeters for indoor localization tasks.

Muhamad Risqi U. Saputra, Pedro P. B. de Gusmao, Yasin Almalioglu et al.

This paper presents a novel method to distill knowledge from a deep pose regressor network for efficient Visual Odometry (VO). Standard distillation relies on "dark knowledge" for successful knowledge transfer. As this knowledge is not available in pose regression and the teacher prediction is not always accurate, we propose to emphasize the knowledge transfer only when we trust the teacher. We achieve this by using teacher loss as a confidence score which places variable relative importance on the teacher prediction. We inject this confidence score to the main training task via Attentive Imitation Loss (AIL) and when learning the intermediate representation of the teacher through Attentive Hint Training (AHT) approach. To the best of our knowledge, this is the first work which successfully distill the knowledge from a deep pose regression network. Our evaluation on the KITTI and Malaga dataset shows that we can keep the student prediction close to the teacher with up to 92.95% parameter reduction and 2.12x faster in computation time.

Yasin Almalioglu, Muhamad Risqi U. Saputra, Pedro P. B. de Gusmao et al.

In the last decade, supervised deep learning approaches have been extensively employed in visual odometry (VO) applications, which is not feasible in environments where labelled data is not abundant. On the other hand, unsupervised deep learning approaches for localization and mapping in unknown environments from unlabelled data have received comparatively less attention in VO research. In this study, we propose a generative unsupervised learning framework that predicts 6-DoF pose camera motion and monocular depth map of the scene from unlabelled RGB image sequences, using deep convolutional Generative Adversarial Networks (GANs). We create a supervisory signal by warping view sequences and assigning the re-projection minimization to the objective loss function that is adopted in multi-view pose estimation and single-view depth generation network. Detailed quantitative and qualitative evaluations of the proposed framework on the KITTI and Cityscapes datasets show that the proposed method outperforms both existing traditional and unsupervised deep VO methods providing better results for both pose estimation and depth recovery.

Mehmet Turan, Yasin Almalioglu, Evin Pinar Ornek et al.

Reliable and real-time 3D reconstruction and localization functionality is a crucial prerequisite for the navigation of actively controlled capsule endoscopic robots as an emerging, minimally invasive diagnostic and therapeutic technology for use in the gastrointestinal (GI) tract. In this study, we propose a fully dense, non-rigidly deformable, strictly real-time, intraoperative map fusion approach for actively controlled endoscopic capsule robot applications which combines magnetic and vision-based localization, with non-rigid deformations based frame-to-model map fusion. The performance of the proposed method is demonstrated using four different ex-vivo porcine stomach models. Across different trajectories of varying speed and complexity, and four different endoscopic cameras, the root mean square surface reconstruction errors 1.58 to 2.17 cm.

Mehmet Turan, Evin Pinar Ornek, Nail Ibrahimli et al.

In the last decade, many medical companies and research groups have tried to convert passive capsule endoscopes as an emerging and minimally invasive diagnostic technology into actively steerable endoscopic capsule robots which will provide more intuitive disease detection, targeted drug delivery and biopsy-like operations in the gastrointestinal(GI) tract. In this study, we introduce a fully unsupervised, real-time odometry and depth learner for monocular endoscopic capsule robots. We establish the supervision by warping view sequences and assigning the re-projection minimization to the loss function, which we adopt in multi-view pose estimation and single-view depth estimation network. Detailed quantitative and qualitative analyses of the proposed framework performed on non-rigidly deformable ex-vivo porcine stomach datasets proves the effectiveness of the method in terms of motion estimation and depth recovery.

Mehmet Turan, Yasin Almalioglu, Hunter Gilbert et al.

In the last decade, researchers and medical device companies have made major advances towards transforming passive capsule endoscopes into active medical robots. One of the major challenges is to endow capsule robots with accurate perception of the environment inside the human body, which will provide necessary information and enable improved medical procedures. We extend the success of deep learning approaches from various research fields to the problem of uncalibrated, asynchronous, and asymmetric sensor fusion for endoscopic capsule robots. The results performed on real pig stomach datasets show that our method achieves sub-millimeter precision for both translational and rotational movements and contains various advantages over traditional sensor fusion techniques.

Mehmet Turan, Yasin Almalioglu, Hunter Gilbert et al.

A reliable, real time multi-sensor fusion functionality is crucial for localization of actively controlled capsule endoscopy robots, which are an emerging, minimally invasive diagnostic and therapeutic technology for the gastrointestinal (GI) tract. In this study, we propose a novel multi-sensor fusion approach based on a particle filter that incorporates an online estimation of sensor reliability and a non-linear kinematic model learned by a recurrent neural network. Our method sequentially estimates the true robot pose from noisy pose observations delivered by multiple sensors. We experimentally test the method using 5 degree-of-freedom (5-DoF) absolute pose measurement by a magnetic localization system and a 6-DoF relative pose measurement by visual odometry. In addition, the proposed method is capable of detecting and handling sensor failures by ignoring corrupted data, providing the robustness expected of a medical device. Detailed analyses and evaluations are presented using ex-vivo experiments on a porcine stomach model prove that our system achieves high translational and rotational accuracies for different types of endoscopic capsule robot trajectories.

Mehmet Turan, Yasin Almalioglu, Helder Araujo et al.

Ingestible wireless capsule endoscopy is an emerging minimally invasive diagnostic technology for inspection of the GI tract and diagnosis of a wide range of diseases and pathologies. Medical device companies and many research groups have recently made substantial progresses in converting passive capsule endoscopes to active capsule robots, enabling more accurate, precise, and intuitive detection of the location and size of the diseased areas. Since a reliable real time pose estimation functionality is crucial for actively controlled endoscopic capsule robots, in this study, we propose a monocular visual odometry (VO) method for endoscopic capsule robot operations. Our method lies on the application of the deep Recurrent Convolutional Neural Networks (RCNNs) for the visual odometry task, where Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) are used for the feature extraction and inference of dynamics across the frames, respectively. Detailed analyses and evaluations made on a real pig stomach dataset proves that our system achieves high translational and rotational accuracies for different types of endoscopic capsule robot trajectories.

Mehmet Turan, Yasin Almalioglu, Hunter Gilbert et al.

A reliable, real-time simultaneous localization and mapping (SLAM) method is crucial for the navigation of actively controlled capsule endoscopy robots. These robots are an emerging, minimally invasive diagnostic and therapeutic technology for use in the gastrointestinal (GI) tract. In this study, we propose a dense, non-rigidly deformable, and real-time map fusion approach for actively controlled endoscopic capsule robot applications. The method combines magnetic and vision based localization, and makes use of frame-to-model fusion and model-to-model loop closure. The performance of the method is demonstrated using an ex-vivo porcine stomach model. Across four trajectories of varying speed and complexity, and across three cameras, the root mean square localization errors range from 0.42 to 1.92 cm, and the root mean square surface reconstruction errors range from 1.23 to 2.39 cm.

Mehmet Turan, Yasin Almalioglu, Helder Araujo et al.

In the gastrointestinal (GI) tract endoscopy field, ingestible wireless capsule endoscopy is considered as a minimally invasive novel diagnostic technology to inspect the entire GI tract and to diagnose various diseases and pathologies. Since the development of this technology, medical device companies and many groups have made significant progress to turn such passive capsule endoscopes into robotic active capsule endoscopes to achieve almost all functions of current active flexible endoscopes. However, the use of robotic capsule endoscopy still has some challenges. One such challenge is the precise localization of such active devices in 3D world, which is essential for a precise three-dimensional (3D) mapping of the inner organ. A reliable 3D map of the explored inner organ could assist the doctors to make more intuitive and correct diagnosis. In this paper, we propose to our knowledge for the first time in literature a visual simultaneous localization and mapping (SLAM) method specifically developed for endoscopic capsule robots. The proposed RGB-Depth SLAM method is capable of capturing comprehensive dense globally consistent surfel-based maps of the inner organs explored by an endoscopic capsule robot in real time. This is achieved by using dense frame-to-model camera tracking and windowed surfelbased fusion coupled with frequent model refinement through non-rigid surface deformations.

Mehmet Turan, Yasin Almalioglu, Ender Konukoglu et al.

We present a robust deep learning based 6 degrees-of-freedom (DoF) localization system for endoscopic capsule robots. Our system mainly focuses on localization of endoscopic capsule robots inside the GI tract using only visual information captured by a mono camera integrated to the robot. The proposed system is a 23-layer deep convolutional neural network (CNN) that is capable to estimate the pose of the robot in real time using a standard CPU. The dataset for the evaluation of the system was recorded inside a surgical human stomach model with realistic surface texture, softness, and surface liquid properties so that the pre-trained CNN architecture can be transferred confidently into a real endoscopic scenario. An average error of 7:1% and 3:4% for translation and rotation has been obtained, respectively. The results accomplished from the experiments demonstrate that a CNN pre-trained with raw 2D endoscopic images performs accurately inside the GI tract and is robust to various challenges posed by reflection distortions, lens imperfections, vignetting, noise, motion blur, low resolution, and lack of unique landmarks to track.