Image database system for glaucoma diagnosis support

Tato práce popisuje přehled standardních a pokročilých metod používaných k diagnose glaukomu v ranném stádiu. Na základě teoretických poznatků je implementován internetově orientovaný informační systém pro oční lékaře, který má tři hlavní cíle. Prvním cílem je možnost sdílení osobních dat konkrétního pacienta bez nutnosti posílat tato data internetem. Druhým cílem je vytvořit účet pacienta založený na kompletním očním vyšetření. Posledním cílem je aplikovat algoritmus pro registraci intenzitního a barevného fundus obrazu a na jeho základě vytvořit internetově orientovanou tři-dimenzionální vizualizaci optického disku. Tato práce je součásti DAAD spolupráce mezi Ústavem Biomedicínského Inženýrství, Vysokého Učení Technického v Brně, Oční klinikou v Erlangenu a Ústavem Informačních Technologií, Friedrich-Alexander University, Erlangen-Nurnberg.This master thesis describes a conception of standard and advanced eye examination methods used for glaucoma diagnosis in its early stage. According to the theoretical knowledge, a web based information system for ophthalmologists with three main aims is implemented. The first aim is the possibility to share medical data of a concrete patient without sending his personal data through the Internet. The second aim is to create a patient account based on a complete eye examination procedure. The last aim is to improve the HRT diagnostic method with an image registration algorithm for the fundus and intensity images and create an optic nerve head web based 3D visualization. This master thesis is a part of project based on DAAD co-operation between Department of Biomedical Engineering, Brno University of Technology, Eye Clinic in Erlangen and Department of Computer Science, Friedrich-Alexander University, Erlangen-Nurnberg.

Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table

M2U-net: Effective and efficient retinal vessel segmentation for real-world applications

In this paper, we present a novel neural network architecture for retinal vessel segmentation that improves over the state of the art on two benchmark datasets, is the first to run in real time on high resolution images, and its small memory and processing requirements make it deployable in mobile and embedded systems. The M2U-Net has a new encoder-decoder architecture that is inspired by the U-Net. It adds pretrained components of MobileNetV2 in the encoder part and novel contractive bottleneck blocks in the decoder part that, combined with bilinear upsampling, drastically reduce the parameter count to 0.55M compared to 31.03M in the original U-Net. We have evaluated its performance against a wide body of previously published results on three public datasets. On two of them, the M2U-Net achieves new state-of-the-art performance by a considerable margin. When implemented on a GPU, our method is the first to achieve real-time inference speeds on high-resolution fundus images. We also implemented our proposed network on an ARM-based embedded system where it segments images in between 0.6 and 15 sec, depending on the resolution. Thus, the M2U-Net enables a number of applications of retinal vessel structure extraction, such as early diagnosis of eye diseases, retinal biometric authentication systems, and robot assisted microsurgery

TPU Cloud-Based Generalized U-Net for Eye Fundus Image Segmentation

Medical images from different clinics are acquired with different instruments and settings. To perform segmentation on these images as a cloud-based service we need to train with multiple datasets to increase the segmentation independency from the source. We also require an ef cient and fast segmentation network. In this work these two problems, which are essential for many practical medical imaging applications, are studied. As a segmentation network, U-Net has been selected. U-Net is a class of deep neural networks which have been shown to be effective for medical image segmentation. Many different U-Net implementations have been proposed.With the recent development of tensor processing units (TPU), the execution times of these algorithms can be drastically reduced. This makes them attractive for cloud services. In this paper, we study, using Google's publicly available colab environment, a generalized fully con gurable Keras U-Net implementation which uses Google TPU processors for training and prediction. As our application problem, we use the segmentation of Optic Disc and Cup, which can be applied to glaucoma detection. To obtain networks with a good performance, independently of the image acquisition source, we combine multiple publicly available datasets (RIM-One V3, DRISHTI and DRIONS). As a result of this study, we have developed a set of functions that allow the implementation of generalized U-Nets adapted to TPU execution and are suitable for cloud-based service implementation.Ministerio de Economía y Competitividad TEC2016-77785-

Arbeiten zur Optischen Kohärenztomographie, Magnetresonanzspektroskopie und Ultrahochfeld-Magnetresonanztomographie

Abstrakt (Deutsch) Hintergrund: Die Multiple Sklerose ist eine der häufigsten neurologischen Erkrankungen, die zu Behinderung bereits im jungen Erwachsenenalter führen kann. Hierzu tragen im Krankheitsprozess sowohl neuroinflammatorische wie auch neurodegenerative Komponenten bei. Moderne bildgebende Verfahren wie die Ultrahochfeld-Magnetresonanztomographie (UHF-MRT), die Optische Kohärenztomographie (OCT) und die Magnetresonanzspektroskopie (MRS) können benutzt werden, um diese neurodegenerativen Prozesse näher zu charakterisieren und im zeitlichen Verlauf zu beobachten. Zielsetzung: Ziel ist es, die genannten Verfahren zur Charakterisierung von Kohorten von MS-Patienten einzusetzen und die Verfahren zueinander, sowie mit klinischen Parametern in Beziehung zu setzen oder diagnostisch zu nutzen. Methodik: Patienten mit Multipler Sklerose oder Neuromyelitis optica wurden klinisch-neurologisch, mit Optischer Kohärenztomographie, Sehprüfungen, Untersuchungen der visuell evozierten Potentiale (VEP), (Ultrahochfeld-) Magnetresonanztomographie und Magnetresonanzspektroskopie untersucht. Ergebnisse: Die in der Studie eingesetzten bildgebenden Verfahren konnten dazu beitragen, Neuroinflammation und Neurodegeneration bei an Multiple Sklerose erkrankten Patienten näher zu charakterisieren. So steht eine mittels OCT messbare Verdünnung retinaler Nervenfaserschichten (RNFL) in Zusammenhang mit dem per MRT gemessenen Hirnparenchymvolumen und Neurodegeneration anzeigenden Parametern, die mithilfe der Magnetresonanzspektroskopie untersucht wurden. Mithilfe der UHF-MRT konnte ein Zusammenhang zwischen dem Volumen und der entzündlichen Läsionslast der Sehstrahlung, der RNFL-Dicke, VEP-Latenzen und Einschränkungen des Sehvermögens dargestellt werden. Außerdem ließen sich mit der UHF-MRT auch neurogenerative Aspekte im Sinne von bleibenden Parenchymdefekten innerhalb entzündlicher Läsionen und einer Verschmächtigung der Sehstrahlung nachweisen und die Detektion insbesondere kortikaler MS-Läsionen wurde im Vergleich zur konventionellen MRT verbessert. Zusammenfassung: OCT, MRS und UHF-MRT sind Verfahren, die eine genauere Beschreibung von Neuroinflammation und Neurodegeneration bei MS-Patienten ermöglichen, wie hier vor allem für die Sehbahn gezeigt wurde. Sie sind nichtinvasiv und lassen sich zur näheren Charakterisierung des aktuellen Zustandes und zur Beobachtung des Krankheitsverlaufs von MS-Patienten benutzen.Abstract (English) Background: Multiple sclerosis (MS) is the most common disabling neurologic disease, that causes impairment in younger people. Both neuroinflammatory and neurodegenerative processes contribute to the pathogenesis of multiple sclerosis. Innovative imaging methods, such as ultra-high field magnetic resonance tomography (UHF-MRI), optic coherence tomography (OCT) and magnetic resonance spectroscopy (MRS) can be used for characterizing these neurodegenerative processes in detail and over time course. Objective: To use the imaging methods mentioned above to further characterize cohorts of MS patients and to correlate the parameters with themselves as well as with clinical parameters and to evaluate their prognostic and diagnostic relevance. Methods: Patients with multiple sclerosis were examined clinically, by OCT, visual acuity testing, examination of visually evoked potentials, ultra high field magnetic resonance tomography and magnetic resonance spectroscopy. Results: The imaging methods used in these studies contributed to further characterize neuroinflammation und neurodegeneration in multiple sclerosis patients. A thinning of the retinal nerve fiber layer (RNFL) is correlated with brain parenchyma volume measured by MRI, and markers indicating ongoing neurodegenerative processes as detected by MRS. Using UHF-MRI, a correlation between optic radiation properties (such as inflammatory lesion load and its volume) and RNFL thickness, VEP latencies and visual impairment could be demonstrated. Furthermore, UHF-MRI demonstrated neurodegenerative aspects such as parenchymal defects within inflammatory lesions, an optic radiation thinning and allowed a more precise detection of MS lesions than conventional MRI, in particular cortical grey matter lesions. Summary: OCT, MRS and UHF-MRI are feasible methods to provide a more detailed description of neuroinflammation and neurodegeneration in MS patients, as demonstrated in these studies particularly for the visual pathway. They are non-invasive and can be utilized for clinical to study the disease course and also in differential diagnostic procedures

Psychiatric Case Record

Bipolar Disorder-Mania: Patient was apparently normal one-month back, Then all of a sudden he developed sleep disturbances –mainly difficult in initiation of sleep. He also started abusing his family members for unwanted things. Subsequently, he started talking excessively and irritable. Sometimes he sings film songs and dances. He used to say that God Supreme exists in himself and so he has all the powers of Almighty. With that superior power he says that he can solve all the problems in this world. He also says that he has invented herbs to keep people young. For the past one week, he talks excessively without having an hour of sleep & wanders here and there & found excessively smoking. He becomes excessively spiritual and goes to near by villages for offering prayers to God. He takes only a little food everyday and he is very much keen in personal cleanliness. Paranoid Schizophrenia: She was apparently normal 8 months back, then she developed sleep disturbances in the form of difficult in falling asleep. She was found talking & smiling to herself at night & day with mirror gazing. She started saying that her neighbour & relatives are planning to kill herself by poisoning. In this context she had frequent quarrels with them and she refused to take food prepared by her mother in law. She left the home at night without informing any one and started wandering in the road side near her home. She was complaining that she hears voices as if her neighbour & relatives were talking about her among themselves She was not doing house hold activities for past 6 months and she was not taking care of her child. Her personal hygiene was very much deteriorated slowly as she used to take bath & brush, only if she was asked to do so. She started abusing & assaulting the strangers and family members. Generalised Anxiety Disorder: Six months back he was apparently normal. He is working as a system analyst in a private bank . He had once, made a mistake in his bank work for which he was given charges by his employer, followed this event he becomes very tense and afraid whenever his boss called him. He is very cautious that he should not commit any mistakes. Even though he is not doing so, he fears that he may commit some mistake in his work. At that moment he develops palpitation, giddiness, breathlessness, excessive sweating over palms and soles. Slowly these symptoms present through out the day even when he was not in his office, and he could not control his fearfulness. For the past 6 months he didn’t sleep well. His sleep is disturbed by bad dreams. Recurrent Depressive Disorder: Patient was apparently alright 2 months back. Then she developed sleep disturbances particularly early morning awakening, she use to wake up by 3.00 am and use to brood about herself and started crying. She was not doing her domestic work as before, as she felt excess tiredness and use to take frequent rests. She developed poor communication. She had lost her interest in pleasurable activities and was not interested in watching TV, and attending family gatherings. She stayed aloof most of the time & calm, quiet and withdrawn. She was expressing her helplessness and hopelessness about the future. She started to have decline in maintaining self care. 15 days back, she frequently expressed suicidal ideas and she had attempted suicide by hanging herself and was rescued by neighbours. 5 days back, she started talking in an irrelevant manner. She was smiling to self. She was assaulting her family members. She was suspicious that her neighbour had done black magic on her and also saying that people are talking about her. She reported hearing the voice of her neighbour scolding and threatening her. Organic Brain Syndrome – Dementia: Ten months back he was apparently alright. Then his relatives noticed himself frequently misplaces things inside his home. Then he started behaving aggressively. He was beating his wife without reason. He was roaming here and there, running out of home and wandering aimlessly. He was not able to come back home when he goes out. He was brought back to home by his relatives. Slowly he developed fearfulness and tremulousness while he was staying alone. He also started saying that his family members & neighbours were talking about himself, in this context he would make frequent quarrels with them. He also started hearing voices of known male voices abusing himself in third person. He sleeps for few hour only. He is passing urine and motion inside the house. He is asking about his brother and mother-in-law who were expired long back. He behaves abnormally such as pouring water in the plate while eating. And his relatives found the symptoms were worsened by evening. All these symptoms started insidiously, increased in severity through time and attained the present state. No history of loss of appetite / crying spells / suicidal tendencies / convulsions / fever / head injury