Evaluation of different segmentation-based approaches for skin disorders from dermoscopic images

Treballs Finals de Grau d'Enginyeria Biomèdica. Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona. Curs: 2022-2023. Tutor/Director: Sala Llonch, Roser, Mata Miquel, Christian, Munuera, JosepSkin disorders are the most common type of cancer in the world and the incident has been lately increasing over the past decades. Even with the most complex and advanced technologies, current image acquisition systems do not permit a reliable identification of the skin lesion by visual examination due to the challenging structure of the malignancy. This promotes the need for the implementation of automatic skin lesion segmentation methods in order to assist in physicians’ diagnostic when determining the lesion's region and to serve as a preliminary step for the classification of the skin lesion. Accurate and precise segmentation is crucial for a rigorous screening and monitoring of the disease's progression. For the purpose of the commented concern, the present project aims to accomplish a state-of-the-art review about the most predominant conventional segmentation models for skin lesion segmentation, alongside with a market analysis examination. With the rise of automatic segmentation tools, a wide number of algorithms are currently being used, but many are the drawbacks when employing them for dermatological disorders due to the high-level presence of artefacts in the image acquired. In light of the above, three segmentation techniques have been selected for the completion of the work: level set method, an algorithm combining GrabCut and k-means methods and an intensity automatic algorithm developed by Hospital Sant Joan de Déu de Barcelona research group. In addition, a validation of their performance is conducted for a further implementation of them in clinical training. The proposals, together with the got outcomes, have been accomplished by means of a publicly available skin lesion image database

Doctor of Philosophy

dissertationUsing eye-tracking technology to capture the visual scanpaths of a sample of laypersons (N = 92), the current study employed a 2 (training condition: ABCDE vs. Ugly Duckling Sign) Ã- 2 (visual condition: photorealistic images vs. illustrations) factorial design to assess whether SSE training succeeds or fails in facilitating increases in sensitivity and specificity. Self-efficacy and perceived importance were tested as moderators, and eye-tracking fixation metrics as mediators, within the framework of Visual Skill Acquisition Theory (VSAT). For sensitivity, results indicated a significant main effect for visual condition, F(1,88) = 7.102, p = .009, wherein illustrations (M = .524, SD = .197) resulted in greater sensitivity than photos (M = .425, SD = .159, d = .55). For specificity, the main effect for training was not significant, F(1,88) = 2.120, p = .149; however, results indicated a significant main effect for visual condition, F(1,88) = 4.079, p = .046, wherein photos (M = .821, SD = .108) resulted in greater specificity than illustrations (M = .770, SD = .137, d = .41). The interaction for training Ã- visual condition, F(1,88) = 3.554, p = .063, was significant within a 90% confidence interval, such that those within the UDS Photo condition displayed greater specificity than all other combinations of training and visual condition. No significant moderated mediation manifested for sensitivity, but for specificity, the model was significant, r = .59, R2 = .34, F(9,82) = 4.7783, p =.001, with Percent of Time in Lookzone serving as a significant mediator, and both self-efficacy and visual condition significantly moderating the mediation. For those in the photo condition with very high self-efficacy, UDS increased specificity directly. For those in the photo condition with self-efficacy levels at the mean or lower, there was a conditional indirect effect through Percent of Time in Lookzoneâ€"which is to say that these individuals spent a larger amount of their viewing time on target (observing the atypical nevi)â€"and time on target is positively related to specificity. Findings suggest that existing SSE training techniques may be enhanced by maximizing visual processing efficiency

Classification of skin disease using deep learning neural networks with mobilenet V2 and LSTM

Deep learning models are efficient in learning the features that assist in understanding complex patterns precisely. This study proposed a computerized process of classifying skin disease through deep learning-based MobileNet V2 and Long Short Term Memory (LSTM). The MobileNet V2 model proved to be efficient with a better accuracy that can work on lightweight computational devices. The proposed model is efficient in maintaining stateful information for precise predictions. A grey-level co-occurrence matrix is used for assessing the progress of diseased growth. The performance has been compared against other state-of-the-art models such as Fine-Tuned Neural Networks (FTNN), Convolutional Neural Network (CNN), Very Deep Convolutional Networks for Large-Scale Image Recognition developed by Visual Geometry Group (VGG), and convolutional neural network architecture that expanded with few changes. The HAM10000 dataset is used and the proposed method has outperformed other methods with more than 85% accuracy. Its robustness in recognizing the affected region much faster with almost 2x lesser computations than the conven-tional MobileNet model results in minimal computational efforts. Furthermore, a mobile application is designed for instant and proper action. It helps the patient and dermatologists identify the type of disease from the affected region’s image at the initial stage of the skin disease. These findings suggest that the proposed system can help general practitioners efficiently and effectively diagnose skin conditions, thereby reducing further complications and morbidity

The evaluation and enhancement of case driven diagnostic advice systems: a study in three domains

Relevant literature has been reviewed regarding the performance, implementation and evaluation of computer based medical decision support systems. The diagnostic performance of five simple case driven acute chest pain advice systems, have been compared using a standardized set of clinical records. A Bayesian inference model demonstrated superiority over two derived by logistic regression. Small data set flow charts performed well but both relied upon the use of expert opinion. A Bayesian acute abdominal pain diagnostic advice system has been evaluated in a clinical trial. Standardized data collection improved the diagnostic performance of doctors. In practice, the computer system offered little additional user benefit. From further tests in primary care, it was concluded that, whereas general practitioners might enhance their performance by using data collection sheets, paramedics might benefit through direct use of the computer. DERMIS is a new dermatology primary care diagnostic advice system. Components include a database derived from 5203 prospectively collected clinical records, a user interface, and an enhanced Bayesian inference model incorporating combined frequency estimates, expert beliefs and rationalized end-point groups. On laboratory testing, the diagnostic accuracy of DERMIS was 83%. The correct diagnosis appeared in the top three, of a possible 42 disease list on 97% of occasions. In a semi-field trial of DERMIS involving 49 general practitioners, doctors did not always collect the same information as a dermatologist but were able to significantly increase their chance of making a correct diagnosis through use of the computer system. It has been concluded that although implementation of DERMIS might well increase general practitioner diagnostic accuracy and lead to improvements in the management of skin disease in primary care, rates of referral for specialist opinion might not be affected unless standard management plans are adopted

Light-tissue interactions for developing portable and wearable optoelectronic devices for sensing of tissue condition, diagnostics and treatment in Photodynamic therapy (PDT)

This thesis presents the development and in-vivo applications of wearable and portable devices for the investigation of light interaction with tissue involved in Photodynamic therapy (PDT) and during contraction of muscles. A hand-held device and a clinical method were developed for time course in-vivo imaging of the fluorescence of the photosensitizer Protoporphyrin IX (PpIX) in healthy and diseased skin with the aim to guide improvement of PDT protocols. The device was used in a small clinical study on 11 healthy volunteers and 13 patients diagnosed with non-melanoma skin cancer (NMSC). Two types of PpIX precursors were administered: Ameluz gel and Metvix® cream. The fluorescence was imaged with a 10 minute time step over three hours which was the recommended metabolism time before commencing PDT treatment at Ninewells Hospital, Dundee. The fluorescence time course was calculated by integrating the areas with the highest intensity. The fluorescence continued to grow in all subjects during the three hours. The time course varied between individuals. There was no statistical significance between either healthy volunteers or patients in Ameluz vs Metvix® groups; nor was there statistical difference between the three lesions groups (Actinic keratosis (AK) Ameluz vs AK Metvix® vs Basal cell carcinoma (BCC) Metvix®). The p-value was larger than 0.05 in a two sample t-test with unequal variances for all the groups. However, there was strong body site dependence between the head & neck compared to the lower leg & feet, or the trunk & hands body site groups (p-value<0.01). One of the possible explanations for this was temperature and vasculature variation in skin at different body sites: the temperature is higher and the vasculature structure is denser at the head and the neck compared to the lower leg or the trunk. The temperature was not measured during the study. So in order to support this hypothesis, typical skin temperatures at the lesion sites were taken from the IR thermal images of healthy skin available in literature. PpIX fluorescence had a positive correlation to temperature. If this hypothesis is true, it will be highly important to PDT treatment. Increasing the temperature could speed up the metabolism and reduce the waiting time before starting the treatment; ambient temperature should be taken into account for daylight PDT; cooling air as pain management should be administered with caution. Potential improvements for wearable PDT light sources were investigated by modelling light transport in skin for the current LED-based Ambulight PDT device, a commercial OLED for future devices and a directional OLED developed in the group. The optical models were implemented in commercial optical software (with intrinsic Monte Carlo ray tracing and Henyey-Greenstein scattering approximation) which was validated on diffuse reflectance and transmittance measurements using in-house made tissue phantoms. The modelling was applied to investigate the benefits from diffusive and forward scattering properties of skin on light transmission in treatment light sources. 1 mm thick skin can only compensate approximately 10% of non-uniform irradiance. It means that uniform illumination is crucial for the treatment light sources. Forward scattering in skin showed a 10% improved light transmission from a collimated emission compared to a wide angle Lambertian emission. However, depth-dependent transmission measurements of directional vs Lambertian emission from organic light emitting films (a nano-imprinted grating was fabricated to provide directional emission in one of the films), collimated vs diffused HeNe laser light through fresh porcine skin did not show the expected improvement. This could be explained by skin roughness which was previously found to change the optical properties and may also affect light coupling. The modelling was applied to guide an optical design of another wearable device – a muscle contraction sensor. Muscle is fibrous and because of that scatters light differently in different directions. The sensor detects the change in backscattered light in parallel and perpendicular directions with respect to muscle fibres. The sensor was implemented on a wearable bandage on fully flexible substrate with flexible OLED and organic photodiodes. The major advantages of organic optoelectronic sensing compared to conventional electromyography (EMG) sensors are the ability to distinguish two types of contractions (isotonic and isometric), insensitivity to electromagnetic interference and the absence of an immune response due to non-invasive electrode-free sensing. Optical modelling was performed to understand the operation of the sensor. A 3D anisotropic optical model of scattering in muscle was created by geometrical manipulations with the standard Henyey-Greenstein scattering volumes. The penetration depth from the Super Yellow OLED was found to be 20-25 mm; the optimal separation between the source and the detector was found to be 20 mm. This distance provided a still detectable signal along with the best discrimination between the two backscatterings. When a 2 mm thick layer of skin and a 2 mm thick layer of adipose tissue were added to the model, the signal was hugely diffused. The discrimination between the two backscatterings decreased by three orders of magnitude, the penetration depth in muscle was reduced, and the intensity of the signal dropped down but was still detectable. With 5 mm thick adipose tissue and 2 mm thick skin the signal was too diffused and interacted with very shallow layers of muscle which approached the limits of the optical sensing of muscle activity

Development of inducible transgenic mouse models for melanoma

Despite many studies on pathology and aetiology during the past decades, the molecular mechanism(s) of melanoma development remains largely unknown. Therefore the purpose of this project was to establish a transgenic mouse model able to investigate the molecular mechanism(s) of melanoma aetiology mediated by N-Ras and PTEN genes. To achieve this, an inducible gene switch approach was employed exploiting the Cre/loxP recombinase system. This approach has the advantage of avoiding embryonic lethality and helps to minimise disease(s) in other tissue(s) that may interfere with animal viability. It was envisaged that this inducible system would establish a model that accurately mimic the development of melanoma in humans. A disadvantage being that the tyrosinase-based promoter was only responsive to the inducer when melanocytes were proliferating. Initially, regulator vectors were created by sub-cloning Cre under the control of a melanocyte-specific promoter either enhanced tyrosinase (EICre) or tyrosinase related protein 2 (Trp2Cre). A Cre responsive, target N-Raslys61 transgene was also cloned, where expression was induced by Cre ablation of ‘Stop' cassette (cmv.stop.N-Raslys61) together with a report target transgene (cmv.stop.EGFP) to aid in expression characterisation. The functional activity and gene-switch specificity of these constructs were subsequently confirmed employing co-transfection of regulator and report target into B16 melanoma cells, but to confirm their activity in primary melanocytes, melanocyte culture conditions had to be defined for optimum growth and transfection as there is no optimized commercial medium available for murine melanocyte culture unlike for human melanocyte. In this study therefore, murine primary melanocyte culture method (50/50) has been defined, which exploited keratinocytes for initial melanocytes growth support as a feed layer. The other advantages of this 50/50 medium were that pigmented cells grew without spontaneous transformation and gave the higher transfection efficiency compared to media exploited by other groups. Using primary melanocytes cultured in 50/50 medium, transgene construction and identification of regulator expression were performed by RT-PCR in vitro prior to in vivo analysis thereby avoiding unnecessary breeding. When concerns had arisen regarding an unexpected lack of melanoma phenotype in vivo particularly in addition of PTEN loss, this culture protocol supplied a successful test of oncogenic potential of N-Raslys61 and PTEN loss in vitro, where N-Raslys61 expression transformed melanocytes and PTEN loss promoted N-Raslys61 to give more aggressive cells. However a functional redundancy was identified, as transformed colonies were not immortalized and eventually senesced, possibly due to their opposing gene functions being on the same signalling pathway; i.e. PTEN fails to provide additional genetic aberrant pathway(s) for the cross-talk with Ras signalling necessary to form malignant tumours. The in vivo experiments commenced by crossing transgenic expressers of EICre regulator with target cmv.stop.N-Raslys61, to generate bigenic EICre/N-Ras mice. Treatment with Ru486 initially apparently failed to exhibit an abnormal phenotype, despite confirmation of N-Raslys61 expression following hair plucking to initiate the hair cycle and anagen melanocytes proliferation, therefore PTENflx/flx mutation was introduced. Unexpectedly, a similar result was obtained following treatment of EICre/PTENflx/flx/N-Raslys61 and EICre/PTENflx/flx in the test of whether PTEN functional loss promoted N-Raslys61 tumourigenesis. However with time, at 12-15 months (systemic) Ru486 treatment, phenotypes of enlarged eyes and harderian gland adenomas were obtained in N-Raslys61 expressing mice, whilst PTEN loss did not produce additional melanocytic phenotype. This confirmation of in vivo activity prompted a more careful analysis of treated mouse skin that discovered the appearance of white hair at treated sites which gave a subtle grey appearance to the coat colour compared to age matched untreated littermates or non-transgenic controls. Subsequent analysis found that melanocyte apoptosis was induced by N-Raslys61 mediated by caspsase-3, and this may explain the lack of melanomas. This new finding implied the existence of a cell defence system to protect mice from oncogenic expression, as a general feature or to overcome specific mutations that have the potential to induce melanoma. Furthermore, the same apoptotic pathway mediated by caspase-3 was mounted against PTEN functional loss. This implied a potential surveillance mechanism to compensate for PTEN function loss and also verified in vivo, the functional redundancy in melanocytes between these two genes observed in vitro, as it may be that until the appropriate anti-apoptotic pathway overcomes this sentinel mechanism, PTEN loss synergism with N-Raslys61 is insufficient for melanoma tumourigenesis. Due to the lack of melanoma, given the well characterized effects of the microenvironment in melanoma development, this study assessed the consequences of keratinocytes disruption. This was achieved employing a keratinocyte-specific K14Cre regulator transgenic line, expressed in proliferative basal cells, hair follicles and stem cells. In Ru486-treated tetragenic compound K14Cre/EICre/cmv.stop.N-Raslys61/PTENflx/flx mice pigmented papillomas were produced. This identified a melanocyte survival loop generated by microenvironment disruption that enabled anagen melanocytes to escape apoptosis during papillomagenesis. Furthermore, the mechanism involved elevated Kit/SCF expression in papillomas. The co-localisation of Kit and TRP-2 positive melanocytes in papilloma basal layers revealed that a Kit/SCF paracrine survival loop resulted in melanocyte survival. These results clearly demonstrated melanocyte cooperation with its immediate microenvironment consistent with the requirement for proliferative keratinocyte support of primary murine melanocyte cultures. Furthermore, these pigmented papillomas, may represent a model relevant to development of human seborrheic keratoses, which are pigmented benign lesions similar to papilloma, and neither nevi nor melanoma (4-6). These murine data suggest that these lesions may arise where papilloma formation occurs alongside anagen and the Kit/SCF paracrine survival loop creates an environment in papillomas sufficient to incorporate the survival and proliferation of anagen melanocytes, although the further studies are necessary to confirm this. To date, most transgenic melanoma models employ H-Ras, with only recent development of a relevant N-Ras model where constitutive, but not inducible, N-Raslys61 expression throughout embryogenesis eventually gave a hyperplastic melanocyte phenotype which is consistent with the report of N-Ras mutation common in congenital nevi but less in acquired nevi (9-13). As with H-Ras models, it appears that the CDKN2A locus deficiency is necessary for melanoma aetiology. In this study, unlike CDKN2A, PTEN loss failed to promote N-Ras melanoma tumourigenesis. This is possibly due to regulating the same signalling pathways, creating a functional redundancy, and the same susceptibility to apoptosis from newly identified potential compensatory surveillance systems. These results show the necessity of cross-talk between multiple genetic pathways to achieve malignant tumour formation and also the advantage of an inducible gene-switch approach to identify useful compensatory systems by allowing addition/deletion of many different interesting genes. Taking the insights from this study further, logically the introduction of p16/p19 deficient mice and/or other melanocyte/melanoma development related genes (specifically not on Ras signalling pathway, e.g. MC1R pathways) would provide an up-to-date, superior mouse model able to mimic molecular aetiology of human melanoma to investigate the functions and mechanisms of other genes such as MITF, B-Raf, MC1R etc involved in the development of human melanoma

Development of Portable Diffuse Optical Spectroscopic Systems For Treatment Monitoring

The goal of this dissertation is to demonstrate the utility of portable, small-scale diffuse optical spectroscopic (DOS) systems for the diagnosis and treatment monitoring of various diseases. These systems employ near-infrared light (wavelength range of 650nm to 950nm) to probe human tissue and are sensitive to changes in scattering and absorption properties of tissues. The absorption is mainly influenced by the components of blood, namely oxy- and deoxy-hemoglobin (HbO2 and Hb) and parameters that can be derived from them (e.g. total hemoglobin concentration [THb] and oxygen saturation, StO2). Therefore, I focused on diseases in which these parameters change, which includes vascular diseases such as Peripheral Atrial Disease (PAD) and Infantile Hemangiomas (IH) as well as musculoskeletal autoimmune diseases such as Rheumatoid Arthritis (RA). In each of these specific diseases, current monitoring techniques are limited by their sensitivity to disease progression or simply do not exist as a quantitative metric. As part of this project, I first designed and built a wireless handheld DOS device (WHDD) that can perform DOS measurements at various tissue depths. This device was used in a 15-patient pilot study for infantile hemangiomas (IH) to differentiate diseased skin from normal skin and monitor the vascular changes during intervention. In another study, I compare the ultra-small form- factor WHDD’s ability to monitor synovitis and disease progression during a patient’s treatment of RA against the capabilities of a proven frequency domain optical tomographic (FDOT) system that has shown to differentiate patients with and without RA. Learning from clinical utility of the WHDD from these two studies, I adapted the WHDD technology to develop a compact multi- channel DOS measurement system to monitor perfusion changes in the lower extremities before and after surgical intervention for patients with peripheral artery disease (PAD). Using this multi- channel system, which we called the vascular optical spectroscopic measurement (VOSM) system, our group conducted a 20-subject pilot study to quantify its ability to monitor blood perfusion before and after revascularization of stenotic arteries in the lower extremities. This proof-of- concept study demonstrated how DOS may help vascular surgeons perform revascularization procedures in the operating room and assists in post-operative treatment monitoring of vascular diseases

Immune regulation in premalignant vulvar and vaginal disorders

During embryogenesis, the external genitalia develop under the influence of hormones. The vulva originates from the genital tubercle (clitoris), urogenital groove (vestibulum), urethral folds (labia minora) and genital swellings (labia majora). Structures belonging to the vulva are the mons pubis, labia majora and minora, the vestibule of the vagina, the hymen, the clitoris and the external urethral orifice. The outer aspects of the vulva are covered with normal cornified skin epithelium, which consists of three layers; the epidermis, dermis and subcutis. The epidermis of labia majora, labia minora and the frenulum of the clitoris is cornified stratified squamous epithelium and is developed from the embryonic ectoderm. It is histologically made up of four layers: the stratum germinativum or basal layer that forms the boundary with the dermis, the stratum spinosum, the stratum granulosum, and the stratum corneum (Fig. 1). The vestibule is lined with mucosal epithelium of endodermal origin, as is the vagina. The vaginal epithelium, however, is derived from the embryonic mesoderm.The transition of cornified epithelium to non-cornified mucous epithelium can be seen in some patients as the Hart’s line. The skin functions as a barrier to protect women from harmful external influences, which is particularly important in the genital area because of exposure to a wide range of bacteria, fungi and viruses. Cells that reside in the skin are keratinocytes, melanocytes, Merkel cells and Langerhans cells (LCs).The latter is an important resident of the epidermis; it is a bone marrow-derived dendritic cell which plays an essential role in the immune surveillance of the skin.5 The role of the immune system is to protect us from potential dangerous microorganisms such as viruses and bacteria. The immune response is a complex interaction between cells, cytokines, chemokines and other soluble proteins. All these players have their own specific role, which is essential for an effective defense against infection