Efficient video indexing for monitoring disease activity and progression in the upper gastrointestinal tract

Endoscopy is a routine imaging technique used for both diagnosis and minimally invasive surgical treatment. While the endoscopy video contains a wealth of information, tools to capture this information for the purpose of clinical reporting are rather poor. In date, endoscopists do not have any access to tools that enable them to browse the video data in an efficient and user friendly manner. Fast and reliable video retrieval methods could for example, allow them to review data from previous exams and therefore improve their ability to monitor disease progression. Deep learning provides new avenues of compressing and indexing video in an extremely efficient manner. In this study, we propose to use an autoencoder for efficient video compression and fast retrieval of video images. To boost the accuracy of video image retrieval and to address data variability like multi-modality and view-point changes, we propose the integration of a Siamese network. We demonstrate that our approach is competitive in retrieving images from 3 large scale videos of 3 different patients obtained against the query samples of their previous diagnosis. Quantitative validation shows that the combined approach yield an overall improvement of 5% and 8% over classical and variational autoencoders, respectively.Comment: Accepted at IEEE International Symposium on Biomedical Imaging (ISBI), 201

Visual Information Retrieval in Endoscopic Video Archives

In endoscopic procedures, surgeons work with live video streams from the inside of their subjects. A main source for documentation of procedures are still frames from the video, identified and taken during the surgery. However, with growing demands and technical means, the streams are saved to storage servers and the surgeons need to retrieve parts of the videos on demand. In this submission we present a demo application allowing for video retrieval based on visual features and late fusion, which allows surgeons to re-find shots taken during the procedure.Comment: Paper accepted at the IEEE/ACM 13th International Workshop on Content-Based Multimedia Indexing (CBMI) in Prague (Czech Republic) between 10 and 12 June 201

Transmission of natural scene images through a multimode fibre

The optical transport of images through a multimode fibre remains an outstanding challenge with applications ranging from optical communications to neuro-imaging. State of the art approaches either involve measurement and control of the full complex field transmitted through the fibre or, more recently, training of artificial neural networks that however, are typically limited to image classes belong to the same class as the training data set. Here we implement a method that statistically reconstructs the inverse transformation matrix for the fibre. We demonstrate imaging at high frame rates, high resolutions and in full colour of natural scenes, thus demonstrating general-purpose imaging capability. Real-time imaging over long fibre lengths opens alternative routes to exploitation for example for secure communication systems, novel remote imaging devices, quantum state control processing and endoscopy

A deep learning framework for quality assessment and restoration in video endoscopy

Endoscopy is a routine imaging technique used for both diagnosis and minimally invasive surgical treatment. Artifacts such as motion blur, bubbles, specular reflections, floating objects and pixel saturation impede the visual interpretation and the automated analysis of endoscopy videos. Given the widespread use of endoscopy in different clinical applications, we contend that the robust and reliable identification of such artifacts and the automated restoration of corrupted video frames is a fundamental medical imaging problem. Existing state-of-the-art methods only deal with the detection and restoration of selected artifacts. However, typically endoscopy videos contain numerous artifacts which motivates to establish a comprehensive solution. We propose a fully automatic framework that can: 1) detect and classify six different primary artifacts, 2) provide a quality score for each frame and 3) restore mildly corrupted frames. To detect different artifacts our framework exploits fast multi-scale, single stage convolutional neural network detector. We introduce a quality metric to assess frame quality and predict image restoration success. Generative adversarial networks with carefully chosen regularization are finally used to restore corrupted frames. Our detector yields the highest mean average precision (mAP at 5% threshold) of 49.0 and the lowest computational time of 88 ms allowing for accurate real-time processing. Our restoration models for blind deblurring, saturation correction and inpainting demonstrate significant improvements over previous methods. On a set of 10 test videos we show that our approach preserves an average of 68.7% which is 25% more frames than that retained from the raw videos.Comment: 14 page

Vision-based retargeting for endoscopic navigation

Endoscopy is a standard procedure for visualising the human gastrointestinal tract. With the advances in biophotonics, imaging techniques such as narrow band imaging, confocal laser endomicroscopy, and optical coherence tomography can be combined with normal endoscopy for assisting the early diagnosis of diseases, such as cancer. In the past decade, optical biopsy has emerged to be an effective tool for tissue analysis, allowing in vivo and in situ assessment of pathological sites with real-time feature-enhanced microscopic images. However, the non-invasive nature of optical biopsy leads to an intra-examination retargeting problem, which is associated with the difficulty of re-localising a biopsied site consistently throughout the whole examination. In addition to intra-examination retargeting, retargeting of a pathological site is even more challenging across examinations, due to tissue deformation and changing tissue morphologies and appearances. The purpose of this thesis is to address both the intra- and inter-examination retargeting problems associated with optical biopsy. We propose a novel vision-based framework for intra-examination retargeting. The proposed framework is based on combining visual tracking and detection with online learning of the appearance of the biopsied site. Furthermore, a novel cascaded detection approach based on random forests and structured support vector machines is developed to achieve efficient retargeting. To cater for reliable inter-examination retargeting, the solution provided in this thesis is achieved by solving an image retrieval problem, for which an online scene association approach is proposed to summarise an endoscopic video collected in the first examination into distinctive scenes. A hashing-based approach is then used to learn the intrinsic representations of these scenes, such that retargeting can be achieved in subsequent examinations by retrieving the relevant images using the learnt representations. For performance evaluation of the proposed frameworks, extensive phantom, ex vivo and in vivo experiments have been conducted, with results demonstrating the robustness and potential clinical values of the methods proposed.Open Acces

Optical techniques for 3D surface reconstruction in computer-assisted laparoscopic surgery

One of the main challenges for computer-assisted surgery (CAS) is to determine the intra-opera- tive morphology and motion of soft-tissues. This information is prerequisite to the registration of multi-modal patient-specific data for enhancing the surgeon’s navigation capabilites by observ- ing beyond exposed tissue surfaces and for providing intelligent control of robotic-assisted in- struments. In minimally invasive surgery (MIS), optical techniques are an increasingly attractive approach for in vivo 3D reconstruction of the soft-tissue surface geometry. This paper reviews the state-of-the-art methods for optical intra-operative 3D reconstruction in laparoscopic surgery and discusses the technical challenges and future perspectives towards clinical translation. With the recent paradigm shift of surgical practice towards MIS and new developments in 3D opti- cal imaging, this is a timely discussion about technologies that could facilitate complex CAS procedures in dynamic and deformable anatomical regions