12 research outputs found
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
New Techniques in Gastrointestinal Endoscopy
As result of progress, endoscopy has became more complex, using more sophisticated devices and has claimed a special form. In this moment, the gastroenterologist performing endoscopy has to be an expert in macroscopic view of the lesions in the gut, with good skills for using standard endoscopes, with good experience in ultrasound (for performing endoscopic ultrasound), with pathology experience for confocal examination. It is compulsory to get experience and to have patience and attention for the follow-up of thousands of images transmitted during capsule endoscopy or to have knowledge in physics necessary for autofluorescence imaging endoscopy. Therefore, the idea of an endoscopist has changed. Examinations mentioned need a special formation, a superior level of instruction, accessible to those who have already gained enough experience in basic diagnostic endoscopy. This is the reason for what these new issues of endoscopy are presented in this book of New techniques in Gastrointestinal Endoscopy
Diffuse Reflectance Spectroscopy to Quantify In Vivo Tissue Optical Properties: Applications in Human Epithelium and Subcutaneous Murine Colon Cancer
Colorectal cancer is the 4th most common and 2nd deadliest cancer. Problems exist with predicting which patients will respond best to certain therapy regimens. Diffuse reflectance spectroscopy has been suggested as a candidate to optically monitor a patient’s early response to therapy and has been received favorably in experimentally managing other cancers such as breast and skin. In this dissertation, two diffuse reflectance spectroscopy probes were designed: one with a combined high-resolution microendoscopy modality, and one that was optimized for acquiring data from subcutaneous murine tumors. For both probes, percent errors for estimating tissue optical properties (reduced scattering coefficient and absorption coefficient) were less than 5% and 10%, respectively. Then, studies on tissue-simulating phantoms were performed to test probe sensitivity and to serve as testing platforms for investigators in biomedical optics. Next, the diffuse reflectance spectroscopy probe was applied to subcutaneous murine colon tumors (n=61) undergoing either antibody immunotherapy or standard 5-fluorouracil chemotherapy. Mice treated with a combination of these therapies showed reduced tumor growth compared to saline control, isotype control, immunotherapy, and chemotherapy groups (p\u3c0.001, \u3c0.001, \u3c0.001, and 0.046, respectively) 7 days post-treatment. Additionally, at 7 days post-treatment, oxyhemoglobin, a marker currently being explored as a functional prognostic cancer marker, trended to increase in immunotherapy, chemotherapy, and combination therapy groups compared to controls (p=0.315, 0.149, and 0.190). Also of interest, an oxyhemoglobin flare (averageincrease of 1.44x from baseline, p=0.03 compared to controls) was shown in tumors treated with chemotherapy, indicating that diffuse reflectance spectroscopy may be useful as a complimentary tool to monitor early tumor therapeutic response in colon cancer. However, subject-to-subject variability was high and studies correlating survival to early oxyhemoglobin flares are suggested
Development of an image guidance system for laparoscopic liver surgery and evaluation of optical and computer vision techniques for the assessment of liver tissue
Introduction: Liver resection is increasingly being carried out via the laparoscopic approach (keyhole surgery) because there is mounting evidence that it benefits patients by reducing pain and length of hospitalisation. There are however ongoing concerns about oncological radicality (i.e. ability to completely remove cancer) and an inability to control massive haemorrhage. These issues can partially be attributed to a loss of sensation such as depth perception, tactile feedback and a reduced field of view. Utilisation of optical imaging and computer vision may be able to compensate for some of the lost sensory input because these modalities can facilitate visualisation of liver tissue and structural anatomy. Their use in laparoscopy is attractive because it is easy to adapt or integrate with existing technology. The aim of this thesis is to explore to what extent this technology can aid in the detection of normal and abnormal liver tissue and structures. / Methods: The current state of the art for optical imaging and computer vision in laparoscopic liver surgery is assessed in a systematic review. Evaluation of confocal laser endomicroscopy is carried out on a murine and porcine model of liver disease. Multispectral near infrared imaging is evaluated on ex-vivo liver specimen. Video magnification is assessed on a mechanical flow phantom and a porcine model of liver disease. The latter model was also employed to develop a computer vision based image guidance system for laparoscopic liver surgery. This image guidance system is further evaluated in a clinical feasibility study. Where appropriate, experimental findings are substantiated with statistical analysis. / Results: Use of confocal laser endomicroscopy enabled discrimination between cancer and normal liver tissue with a sub-millimetre precision. This technology also made it possible to verify the adequacy of thermal liver ablation. Multispectral imaging, at specific wavelengths was shown to have the potential to highlight the presence of colorectal and hepatocellular cancer. An image reprocessing algorithm is proposed to simplify visual interpretation of the resulting images. It is shown that video magnification can determine the presence of pulsatile motion but that it cannot reliably determine the extent of motion. Development and performance metrics of an image guidance system for laparoscopic liver surgery are outlined. The system was found to improve intraoperative orientation more development work is however required to enable reliable prediction of oncological margins. / Discussion: The results in this thesis indicate that confocal laser endomicroscopy and image guidance systems have reached a development stage where their intraoperative use may benefit surgeons by visualising features of liver anatomy and tissue characteristics. Video magnification and multispectral imaging require more development and suggestions are made to direct this work. It is also highlighted that it is crucial to standardise assessment methods for these technologies which will allow a more direct comparison between the outcomes of different groups. Limited imaging depth is a major restriction of these technologies but this may be overcome by combining them with preoperatively obtained imaging data. Just like laparoscopy, optical imaging and computer vision use functions of light, a shared characteristic that makes their combined use complementary
Retrieval and Registration of Long-Range Overlapping Frames for Scalable Mosaicking of In Vivo Fetoscopy
Purpose: The standard clinical treatment of Twin-to-Twin Transfusion Syndrome
consists in the photo-coagulation of undesired anastomoses located on the
placenta which are responsible to a blood transfer between the two twins. While
being the standard of care procedure, fetoscopy suffers from a limited
field-of-view of the placenta resulting in missed anastomoses. To facilitate
the task of the clinician, building a global map of the placenta providing a
larger overview of the vascular network is highly desired. Methods: To overcome
the challenging visual conditions inherent to in vivo sequences (low contrast,
obstructions or presence of artifacts, among others), we propose the following
contributions: (i) robust pairwise registration is achieved by aligning the
orientation of the image gradients, and (ii) difficulties regarding long-range
consistency (e.g. due to the presence of outliers) is tackled via a bag-of-word
strategy, which identifies overlapping frames of the sequence to be registered
regardless of their respective location in time. Results: In addition to visual
difficulties, in vivo sequences are characterised by the intrinsic absence of
gold standard. We present mosaics motivating qualitatively our methodological
choices and demonstrating their promising aspect. We also demonstrate
semi-quantitatively, via visual inspection of registration results, the
efficacy of our registration approach in comparison to two standard baselines.
Conclusion: This paper proposes the first approach for the construction of
mosaics of placenta in in vivo fetoscopy sequences. Robustness to visual
challenges during registration and long-range temporal consistency are
proposed, offering first positive results on in vivo data for which standard
mosaicking techniques are not applicable.Comment: Accepted for publication in International Journal of Computer
Assisted Radiology and Surgery (IJCARS
Motion-Aware Mosaicing for Confocal Laser Endomicroscopy
International audienceProbe-based Confocal Laser Endomicroscopy (pCLE) provides physicians with real-time access to histological information during standard endoscopy procedures, through high-resolution cellular imaging of internal tissues. Earlier work on mosaicing has enhanced the potential of this imaging modality by meeting the need to get a complete representation of the imaged region. However, with approaches, the dynamic information, which may be of clinical interest, is lost. In this study, we propose a new mosaic construction algorithm for pCLE sequences based on a min-cut optimization and gradient-domain composition. Its main advantage is that the motion of some structures within the tissue such as blood cells in capillaries, is taken into account. This allows physicians to get both a sharper static representation and a dynamic representation of the imaged tissue. Results on 16 sequences acquired in vivo on six different organs demonstrate the clinical relevance of our approach
Motion-Aware Mosaicing for Confocal Laser Endomicroscopy
Probe-based Confocal Laser Endomicroscopy (pCLE) pro- vides physicians with real-time access to histological information during standard endoscopy procedures, through high-resolution cellular imaging of internal tissues. Earlier work on mosaicing has enhanced the potential of this imaging modality by meeting the need to get a complete representation of the imaged region. However, with approaches, the dynamic information, which may be of clinical interest, is lost. In this study, we propose a new mosaic construction algorithm for pCLE sequences based on a min-cut optimization and gradient-domain composition. Its main advantage is that the motion of some structures within the tissue such as blood cells in capillaries, is taken into account. This allows physicians to get both a sharper static representation and a dynamic representation of the imaged tissue. Results on 16 sequences acquired in vivo on six different organs demonstrate the clinical relevance of our approach
An Investigation of the Diagnostic Potential of Autofluorescence Lifetime Spectroscopy and Imaging for Label-Free Contrast of Disease
The work presented in this thesis aimed to study the application of fluorescence lifetime spectroscopy (FLS) and fluorescence lifetime imaging microscopy (FLIM) to investigate their potential for diagnostic contrast of diseased tissue with a particular emphasis on autofluorescence (AF) measurements of gastrointestinal (GI) disease.
Initially, an ex vivo study utilising confocal FLIM was undertaken with 420 nm excitation to characterise the fluorescence lifetime (FL) images obtained from 71 GI samples from 35 patients. A significant decrease in FL was observed between normal colon and polyps (p = 0.024), and normal colon and inflammatory bowel disease (IBD) (p = 0.015). Confocal FLIM was also performed on 23 bladder samples. A longer, although not significant, FL for cancer was observed, in paired specimens (n = 5) instilled with a photosensitizer.
The first in vivo study was a clinical investigation of skin cancer using a fibre-optic FL spectrofluorometer and involved the interrogation of 27 lesions from 25 patients. A significant decrease in the FL of basal cell carcinomas compared to healthy tissue was observed (p = 0.002) with 445 nm excitation.
A novel clinically viable FLS fibre-optic probe was then applied ex vivo to measure 60 samples collected from 23 patients. In a paired analysis of neoplastic polyps and normal colon obtained from the same region of the colon in the same patient (n = 12), a significant decrease in FL was observed (p = 0.021) with 435 nm excitation. In contrast, with 375 nm excitation, the mean FL of IBD specimens (n = 4) was found to be longer than that of normal tissue, although not statistically significant. Finally, the FLS system was applied in vivo in 17 patients, with initial data indicating that 435 nm excitation results in AF lifetimes that are broadly consistent with ex vivo studies, although no diagnostically significant differences were observed in the signals obtained in vivo.Open Acces