Online Super-Resolution For Fibre-Bundle-Based Confocal Laser Endomicroscopy

Probe-based Confocal Laser Endomicroscopy (pCLE) produces microscopic images enabling real-time in vivo optical biopsy. However, the miniaturisation of the optical hardware, specifically the reliance on an optical fibre bundle as an imaging guide, fundamentally limits image quality by producing artefacts, noise, and relatively low contrast and resolution. The reconstruction approaches in clinical pCLE products do not fully alleviate these problems. Consequently, image quality remains a barrier that curbs the full potential of pCLE. Enhancing the image quality of pCLE in real-time remains a challenge. The research in this thesis is a response to this need. I have developed dedicated online super-resolution methods that account for the physics of the image acquisition process. These methods have the potential to replace existing reconstruction algorithms without interfering with the fibre design or the hardware of the device. In this thesis, novel processing pipelines are proposed for enhancing the image quality of pCLE. First, I explored a learning-based super-resolution method that relies on mapping from the low to the high-resolution space. Due to the lack of high-resolution pCLE, I proposed to simulate high-resolution data and use it as a ground truth model that is based on the pCLE acquisition physics. However, pCLE images are reconstructed from irregularly distributed fibre signals, and grid-based Convolutional Neural Networks are not designed to take irregular data as input. To alleviate this problem, I designed a new trainable layer that embeds Nadaraya- Watson regression. Finally, I proposed a novel blind super-resolution approach by deploying unsupervised zero-shot learning accompanied by a down-sampling kernel crafted for pCLE. I evaluated these new methods in two ways: a robust image quality assessment and a perceptual quality test assessed by clinical experts. The results demonstrate that the proposed super-resolution pipelines are superior to the current reconstruction algorithm in terms of image quality and clinician preference

LLCaps: Learning to Illuminate Low-Light Capsule Endoscopy with Curved Wavelet Attention and Reverse Diffusion

Wireless capsule endoscopy (WCE) is a painless and non-invasive diagnostic tool for gastrointestinal (GI) diseases. However, due to GI anatomical constraints and hardware manufacturing limitations, WCE vision signals may suffer from insufficient illumination, leading to a complicated screening and examination procedure. Deep learning-based low-light image enhancement (LLIE) in the medical field gradually attracts researchers. Given the exuberant development of the denoising diffusion probabilistic model (DDPM) in computer vision, we introduce a WCE LLIE framework based on the multi-scale convolutional neural network (CNN) and reverse diffusion process. The multi-scale design allows models to preserve high-resolution representation and context information from low-resolution, while the curved wavelet attention (CWA) block is proposed for high-frequency and local feature learning. Furthermore, we combine the reverse diffusion procedure to further optimize the shallow output and generate the most realistic image. The proposed method is compared with ten state-of-the-art (SOTA) LLIE methods and significantly outperforms quantitatively and qualitatively. The superior performance on GI disease segmentation further demonstrates the clinical potential of our proposed model. Our code is publicly accessible.Comment: To appear in MICCAI 2023. Code availability: https://github.com/longbai1006/LLCap

Zero-shot super-resolution with a physically-motivated downsampling kernel for endomicroscopy

Super-resolution (SR) methods have seen significant advances thanks to the development of convolutional neural networks (CNNs). CNNs have been successfully employed to improve the quality of endomicroscopy imaging. Yet, the inherent limitation of research on SR in endomicroscopy remains the lack of ground truth high-resolution (HR) images, commonly used for both supervised training and reference-based image quality assessment (IQA). Therefore, alternative methods, such as unsupervised SR are being explored. To address the need for non-reference image quality improvement, we designed a novel zero-shot super-resolution (ZSSR) approach that relies only on the endomicroscopy data to be processed in a self-supervised manner without the need for ground-truth HR images. We tailored the proposed pipeline to the idiosyncrasies of endomicroscopy by introducing both: a physically-motivated Voronoi downscaling kernel accounting for the endomicroscope’s irregular fibre-based sampling pattern, and realistic noise patterns. We also took advantage of video sequences to exploit a sequence of images for self-supervised zero-shot image quality improvement. We run ablation studies to assess our contribution in regards to the downscaling kernel and noise simulation. We validate our methodology on both synthetic and original data. Synthetic experiments were assessed with reference-based IQA, while our results for original images were evaluated in a user study conducted with both expert and non-expert observers. The results demonstrated superior performance in image quality of ZSSR reconstructions in comparison to the baseline method. The ZSSR is also competitive when compared to supervised single-image SR, especially being the preferred reconstruction technique by experts

A deep-learning-based approach for aircraft engine defect detection

Borescope inspection is a labour-intensive process used to find defects in aircraft engines that contain areas not visible during a general visual inspection. The outcome of the process largely depends on the judgment of the maintenance professionals who perform it. This research develops a novel deep learning framework for automated borescope inspection. In the framework, a customised U-Net architecture is developed to detect the defects on high-pressure compressor blades. Since motion blur is introduced in some images while the blades are rotated during the inspection, a hybrid motion deblurring method for image sharpening and denoising is applied to remove the effect based on classic computer vision techniques in combination with a customised GAN model. The framework also addresses the data imbalance, small size of the defects and data availability issues in part by testing different loss functions and generating synthetic images using a customised generative adversarial net (GAN) model, respectively. The results obtained from the implementation of the deep learning framework achieve precisions and recalls of over 90%. The hybrid model for motion deblurring results in a 10× improvement in image quality. However, the framework only achieves modest success with particular loss functions for very small sizes of defects. The future study will focus on very small defects detection and extend the deep learning framework to general borescope inspection.Engineering and Physical Sciences Research Council (EPSRC): 11317

Bayesian image restoration and bacteria detection in optical endomicroscopy

Optical microscopy systems can be used to obtain high-resolution microscopic images of tissue cultures and ex vivo tissue samples. This imaging technique can be translated for in vivo, in situ applications by using optical fibres and miniature optics. Fibred optical endomicroscopy (OEM) can enable optical biopsy in organs inaccessible by any other imaging systems, and hence can provide rapid and accurate diagnosis in a short time. The raw data the system produce is difficult to interpret as it is modulated by a fibre bundle pattern, producing what is called the “honeycomb effect”. Moreover, the data is further degraded due to the fibre core cross coupling problem. On the other hand, there is an unmet clinical need for automatic tools that can help the clinicians to detect fluorescently labelled bacteria in distal lung images. The aim of this thesis is to develop advanced image processing algorithms that can address the above mentioned problems. First, we provide a statistical model for the fibre core cross coupling problem and the sparse sampling by imaging fibre bundles (honeycomb artefact), which are formulated here as a restoration problem for the first time in the literature. We then introduce a non-linear interpolation method, based on Gaussian processes regression, in order to recover an interpretable scene from the deconvolved data. Second, we develop two bacteria detection algorithms, each of which provides different characteristics. The first approach considers joint formulation to the sparse coding and anomaly detection problems. The anomalies here are considered as candidate bacteria, which are annotated with the help of a trained clinician. Although this approach provides good detection performance and outperforms existing methods in the literature, the user has to carefully tune some crucial model parameters. Hence, we propose a more adaptive approach, for which a Bayesian framework is adopted. This approach not only outperforms the proposed supervised approach and existing methods in the literature but also provides computation time that competes with optimization-based methods

Vedel-objektiiv abil salvestatud kaugseire piltide analüüs kasutades super-resolutsiooni meetodeid

Väitekirja elektrooniline versioon ei sisalda publikatsiooneKäesolevas doktoritöös uuriti nii riist- kui ka tarkvaralisi lahendusi piltide töötlemiseks. Riist¬varalise poole pealt pakuti lahenduseks uudset vedelläätse, milles on dielekt¬rilisest elastomeerist kihilise täituriga membraan otse optilisel teljel. Doktoritöö käigus arendati välja kaks prototüüpi kahe erineva dielektrilisest elastomeerist ki¬hilise täituriga, mille aktiivne ala oli ühel juhul 40 ja teisel 20 mm. Läätse töö vas¬tas elastomeeri deformatsiooni mehaanikale ja suhtelistele muutustele fookuskau¬guses. Muutuste demonstreerimiseks meniskis ja läätse fookuskauguse mõõtmiseks kasutati laserkiirt. Katseandmetest selgub, et muutuste tekitamiseks on vajalik pinge vahemikus 50 kuni 750 volti. Tarkvaralise poole pealt pakuti uut satelliitpiltide parandamise süsteemi. Paku¬tud süsteem jagas mürase sisendpildi DT-CWT laineteisenduse abil mitmeteks sagedusalamribadeks. Pärast müra eemaldamist LA-BSF funktsiooni abil suu¬rendati pildi resolutsiooni DWT-ga ja kõrgsagedusliku alamriba piltide interpo¬leerimisega. Interpoleerimise faktor algsele pildile oli pool sellest, mida kasutati kõrgsagedusliku alamriba piltide interpoleerimisel ning superresolutsiooniga pilt rekonst¬rueeriti IDWT abil. Käesolevas doktoritöös pakuti tarkvaraliseks lahenduseks uudset sõnastiku baasil töötavat super-resolutsiooni (SR) meetodit, milles luuakse paarid suure resolutsiooniga (HR) ja madala resolut-siooniga (LR) piltidest. Kõigepealt jagati vastava sõnastiku loomiseks HR ja LR paarid omakorda osadeks. Esialgse HR kujutise saamiseks LR sisendpildist kombineeriti HR osi. HR osad valiti sõnastikust nii, et neile vastavad LR osad oleksid võimalikult lähedased sisendiks olevale LR pil¬dile. Iga valitud HR osa heledust korrigeeriti, et vähendada kõrvuti asuvate osade heleduse erine¬vusi superresolutsiooniga pildil. Plokkide efekti vähendamiseks ar¬vutati saadud SR pildi keskmine ning bikuupinterpolatsiooni pilt. Lisaks pakuti käesolevas doktoritöös välja kernelid, mille tulemusel on võimalik saadud SR pilte teravamaks muuta. Pakutud kernelite tõhususe tõestamiseks kasutati [83] ja [50] poolt pakutud resolutsiooni parandamise meetodeid. Superreso¬lutsiooniga pilt saadi iga kerneli tehtud HR pildi kombineerimise teel alpha blen¬dingu meetodit kasutades. Pakutud meetodeid ja kerneleid võrreldi erinevate tavaliste ja kaasaegsete meetoditega. Kvantita-tiivsetest katseandmetest ja saadud piltide kvaliteedi visuaal¬sest hindamisest selgus, et pakutud meetodid on tavaliste kaasaegsete meetoditega võrreldes paremad.In this thesis, a study of both hardware and software solutions for image enhance¬ment has been done. On the hardware side, a new liquid lens design with a DESA membrane located directly in the optical path has been demonstrated. Two pro¬totypes with two different DESA, which have a 40 and 20 mm active area in diameter, were developed. The lens performance was consistent with the mechan¬ics of elastomer deformation and relative focal length changes. A laser beam was used to show the change in the meniscus and to measure the focal length of the lens. The experimental results demonstrate that voltage in the range of 50 to 750 V is required to create change in the meniscus. On the software side, a new satellite image enhancement system was proposed. The proposed technique decomposed the noisy input image into various frequency subbands by using DT-CWT. After removing the noise by applying the LA-BSF technique, its resolution was enhanced by employing DWT and interpolating the high-frequency subband images. An original image was interpolated with half of the interpolation factor used for interpolating the high-frequency subband images, and the super-resolved image was reconstructed by using IDWT. A novel single-image SR method based on a generating dictionary from pairs of HR and their corresponding LR images was proposed. Firstly, HR and LR pairs were divided into patches in order to make HR and LR dictionaries respectively. The initial HR representation of an input LR image was calculated by combining the HR patches. These HR patches are chosen from the HR dictionary corre-sponding to the LR patches that have the closest distance to the patches of the in¬put LR image. Each selected HR patch was processed further by passing through an illumination enhancement processing order to reduce the noticeable change of illumination between neighbor patches in the super-resolved image. In order to reduce the blocking effect, the average of the obtained SR image and the bicubic interpolated image was calculated. The new kernels for sampling have also been proposed. The kernels can improve the SR by resulting in a sharper image. In order to demonstrate the effectiveness of the proposed kernels, the techniques from [83] and [50] for resolution enhance¬ment were adopted. The super-resolved image was achieved by combining the HR images produced by each of the proposed kernels using the alpha blending tech-nique. The proposed techniques and kernels are compared with various conventional and state-of-the-art techniques, and the quantitative test results and visual results on the final image quality show the superiority of the proposed techniques and ker¬nels over conventional and state-of-art technique

Machine Learning/Deep Learning in Medical Image Processing

Many recent studies on medical image processing have involved the use of machine learning (ML) and deep learning (DL). This special issue, “Machine Learning/Deep Learning in Medical Image Processing”, has been launched to provide an opportunity for researchers in the area of medical image processing to highlight recent developments made in their fields with ML/DL. Seven excellent papers that cover a wide variety of medical/clinical aspects are selected in this special issue

Automated Prediction of the Response to Neoadjuvant Chemoradiotherapy in Patients Affected by Rectal Cancer

Simple Summary Colorectal cancer is the second most malignant tumor per number of deaths after lung cancer and the third per number of new cases after breast and lung cancer. The correct and rapid identification (i.e., segmentation of the cancer regions) is a fundamental task for correct patient diagnosis. In this study, we propose a novel automated pipeline for the segmentation of MRI scans of patients with LARC in order to predict the response to nCRT using radiomic features. This study involved the retrospective analysis of T-2-weighted MRI scans of 43 patients affected by LARC. The segmentation of tumor areas was on par or better than the state-of-the-art results, but required smaller sample sizes. The analysis of radiomic features allowed us to predict the TRG score, which agreed with the state-of-the-art results. Background: Rectal cancer is a malignant neoplasm of the large intestine resulting from the uncontrolled proliferation of the rectal tract. Predicting the pathologic response of neoadjuvant chemoradiotherapy at an MRI primary staging scan in patients affected by locally advanced rectal cancer (LARC) could lead to significant improvement in the survival and quality of life of the patients. In this study, the possibility of automatizing this estimation from a primary staging MRI scan, using a fully automated artificial intelligence-based model for the segmentation and consequent characterization of the tumor areas using radiomic features was evaluated. The TRG score was used to evaluate the clinical outcome. Methods: Forty-three patients under treatment in the IRCCS Sant'Orsola-Malpighi Polyclinic were retrospectively selected for the study; a U-Net model was trained for the automated segmentation of the tumor areas; the radiomic features were collected and used to predict the tumor regression grade (TRG) score. Results: The segmentation of tumor areas outperformed the state-of-the-art results in terms of the Dice score coefficient or was comparable to them but with the advantage of considering mucinous cases. Analysis of the radiomic features extracted from the lesion areas allowed us to predict the TRG score, with the results agreeing with the state-of-the-art results. Conclusions: The results obtained regarding TRG prediction using the proposed fully automated pipeline prove its possible usage as a viable decision support system for radiologists in clinical practice