372 research outputs found
Deep Learning Techniques for Automated Analysis and Processing of High Resolution Medical Imaging
Programa Oficial de Doutoramento en Computación . 5009V01[Abstract]
Medical imaging plays a prominent role in modern clinical practice for numerous
medical specialties. For instance, in ophthalmology, different imaging techniques are
commonly used to visualize and study the eye fundus. In this context, automated
image analysis methods are key towards facilitating the early diagnosis and adequate
treatment of several diseases. Nowadays, deep learning algorithms have already
demonstrated a remarkable performance for different image analysis tasks. However,
these approaches typically require large amounts of annotated data for the training
of deep neural networks. This complicates the adoption of deep learning approaches,
especially in areas where large scale annotated datasets are harder to obtain, such
as in medical imaging.
This thesis aims to explore novel approaches for the automated analysis of medical
images, particularly in ophthalmology. In this regard, the main focus is on
the development of novel deep learning-based approaches that do not require large
amounts of annotated training data and can be applied to high resolution images.
For that purpose, we have presented a novel paradigm that allows to take advantage
of unlabeled complementary image modalities for the training of deep neural
networks. Additionally, we have also developed novel approaches for the detailed
analysis of eye fundus images. In that regard, this thesis explores the analysis of
relevant retinal structures as well as the diagnosis of different retinal diseases. In
general, the developed algorithms provide satisfactory results for the analysis of the
eye fundus, even when limited annotated training data is available.[Resumen]
Las técnicas de imagen tienen un papel destacado en la práctica clínica moderna
de numerosas especialidades médicas. Por ejemplo, en oftalmología es común el uso
de diferentes técnicas de imagen para visualizar y estudiar el fondo de ojo. En este
contexto, los métodos automáticos de análisis de imagen son clave para facilitar
el diagnóstico precoz y el tratamiento adecuado de diversas enfermedades. En la
actualidad, los algoritmos de aprendizaje profundo ya han demostrado un notable
rendimiento en diferentes tareas de análisis de imagen. Sin embargo, estos métodos
suelen necesitar grandes cantidades de datos etiquetados para el entrenamiento de
las redes neuronales profundas. Esto complica la adopción de los métodos de aprendizaje
profundo, especialmente en áreas donde los conjuntos masivos de datos etiquetados
son más difíciles de obtener, como es el caso de la imagen médica.
Esta tesis tiene como objetivo explorar nuevos métodos para el análisis automático de imagen médica, concretamente en oftalmología. En este sentido, el foco
principal es el desarrollo de nuevos métodos basados en aprendizaje profundo que no
requieran grandes cantidades de datos etiquetados para el entrenamiento y puedan
aplicarse a imágenes de alta resolución. Para ello, hemos presentado un nuevo
paradigma que permite aprovechar modalidades de imagen complementarias no etiquetadas
para el entrenamiento de redes neuronales profundas. Además, también
hemos desarrollado nuevos métodos para el análisis en detalle de las imágenes del
fondo de ojo. En este sentido, esta tesis explora el análisis de estructuras retinianas
relevantes, así como el diagnóstico de diferentes enfermedades de la retina. En
general, los algoritmos desarrollados proporcionan resultados satisfactorios para el
análisis de las imágenes de fondo de ojo, incluso cuando la disponibilidad de datos
de entrenamiento etiquetados es limitada.[Resumo]
As técnicas de imaxe teñen un papel destacado na práctica clínica moderna de
numerosas especialidades médicas. Por exemplo, en oftalmoloxía é común o uso
de diferentes técnicas de imaxe para visualizar e estudar o fondo de ollo. Neste
contexto, os métodos automáticos de análises de imaxe son clave para facilitar o
diagn ostico precoz e o tratamento adecuado de diversas enfermidades. Na actualidade,
os algoritmos de aprendizaxe profunda xa demostraron un notable rendemento
en diferentes tarefas de análises de imaxe. Con todo, estes métodos adoitan necesitar
grandes cantidades de datos etiquetos para o adestramento das redes neuronais
profundas. Isto complica a adopción dos métodos de aprendizaxe profunda, especialmente
en áreas onde os conxuntos masivos de datos etiquetados son máis difíciles
de obter, como é o caso da imaxe médica.
Esta tese ten como obxectivo explorar novos métodos para a análise automática
de imaxe médica, concretamente en oftalmoloxía. Neste sentido, o foco principal
é o desenvolvemento de novos métodos baseados en aprendizaxe profunda que non
requiran grandes cantidades de datos etiquetados para o adestramento e poidan aplicarse
a imaxes de alta resolución. Para iso, presentamos un novo paradigma que
permite aproveitar modalidades de imaxe complementarias non etiquetadas para o
adestramento de redes neuronais profundas. Ademais, tamén desenvolvemos novos
métodos para a análise en detalle das imaxes do fondo de ollo. Neste sentido, esta
tese explora a análise de estruturas retinianas relevantes, así como o diagnóstico de
diferentes enfermidades da retina. En xeral, os algoritmos desenvolvidos proporcionan
resultados satisfactorios para a análise das imaxes de fondo de ollo, mesmo
cando a dispoñibilidade de datos de adestramento etiquetados é limitada
Improving foveal avascular zone segmentation in fluorescein angiograms by leveraging manual vessel labels from public color fundus pictures
In clinical routine, ophthalmologists frequently analyze the shape and size of the foveal avascular zone (FAZ) to detect and monitor retinal diseases. In order to extract those parameters, the contours of the FAZ need to be segmented, which is normally achieved by analyzing the retinal vasculature (RV) around the macula in fluorescein angiograms (FA). Computer-aided segmentation methods based on deep learning (DL) can automate this task. However, current approaches for segmenting the FAZ are often tailored to a specific dataset or require manual initialization. Furthermore, they do not take the variability and challenges of clinical FA into account, which are often of low quality and difficult to analyze. In this paper we propose a DL-based framework to automatically segment the FAZ in challenging FA scans from clinical routine. Our approach mimics the workflow of retinal experts by using additional RV labels as a guidance during training. Hence, our model is able to produce RV segmentations simultaneously. We minimize the annotation work by using a multi-modal approach that leverages already available public datasets of color fundus pictures (CFPs) and their respective manual RV labels. Our experimental evaluation on two datasets with FA from 1) clinical routine and 2) large multicenter clinical trials shows that the addition of weak RV labels as a guidance during training improves the FAZ segmentation significantly with respect to using only manual FAZ annotations.Fil: Hofer, Dominik. Medizinische Universität Wien; AustriaFil: Schmidt Erfurth, Ursula. Medizinische Universität Wien; AustriaFil: Orlando, José Ignacio. Universidad Nacional del Centro de la Provincia de Buenos Aires. Facultad de Ciencias Exactas. Grupo de Plasmas Densos Magnetizados. Provincia de Buenos Aires. Gobernación. Comision de Investigaciones Científicas. Grupo de Plasmas Densos Magnetizados; Argentina. Medizinische Universität Wien; AustriaFil: Goldbach, Felix. Medizinische Universität Wien; AustriaFil: Gerendas, Bianca S.. Medizinische Universität Wien; AustriaFil: Seeböck, Philipp. Medizinische Universität Wien; Austri
Deep Representation Learning with Limited Data for Biomedical Image Synthesis, Segmentation, and Detection
Biomedical imaging requires accurate expert annotation and interpretation that can aid medical staff and clinicians in automating differential diagnosis and solving underlying health conditions. With the advent of Deep learning, it has become a standard for reaching expert-level performance in non-invasive biomedical imaging tasks by training with large image datasets. However, with the need for large publicly available datasets, training a deep learning model to learn intrinsic representations becomes harder. Representation learning with limited data has introduced new learning techniques, such as Generative Adversarial Networks, Semi-supervised Learning, and Self-supervised Learning, that can be applied to various biomedical applications. For example, ophthalmologists use color funduscopy (CF) and fluorescein angiography (FA) to diagnose retinal degenerative diseases. However, fluorescein angiography requires injecting a dye, which can create adverse reactions in the patients. So, to alleviate this, a non-invasive technique needs to be developed that can translate fluorescein angiography from fundus images. Similarly, color funduscopy and optical coherence tomography (OCT) are also utilized to semantically segment the vasculature and fluid build-up in spatial and volumetric retinal imaging, which can help with the future prognosis of diseases. Although many automated techniques have been proposed for medical image segmentation, the main drawback is the model's precision in pixel-wise predictions. Another critical challenge in the biomedical imaging field is accurately segmenting and quantifying dynamic behaviors of calcium signals in cells. Calcium imaging is a widely utilized approach to studying subcellular calcium activity and cell function; however, large datasets have yielded a profound need for fast, accurate, and standardized analyses of calcium signals. For example, image sequences from calcium signals in colonic pacemaker cells ICC (Interstitial cells of Cajal) suffer from motion artifacts and high periodic and sensor noise, making it difficult to accurately segment and quantify calcium signal events. Moreover, it is time-consuming and tedious to annotate such a large volume of calcium image stacks or videos and extract their associated spatiotemporal maps. To address these problems, we propose various deep representation learning architectures that utilize limited labels and annotations to address the critical challenges in these biomedical applications. To this end, we detail our proposed semi-supervised, generative adversarial networks and transformer-based architectures for individual learning tasks such as retinal image-to-image translation, vessel and fluid segmentation from fundus and OCT images, breast micro-mass segmentation, and sub-cellular calcium events tracking from videos and spatiotemporal map quantification. We also illustrate two multi-modal multi-task learning frameworks with applications that can be extended to other domains of biomedical applications. The main idea is to incorporate each of these as individual modules to our proposed multi-modal frameworks to solve the existing challenges with 1) Fluorescein angiography synthesis, 2) Retinal vessel and fluid segmentation, 3) Breast micro-mass segmentation, and 4) Dynamic quantification of calcium imaging datasets
Data efficient deep learning for medical image analysis: A survey
The rapid evolution of deep learning has significantly advanced the field of
medical image analysis. However, despite these achievements, the further
enhancement of deep learning models for medical image analysis faces a
significant challenge due to the scarcity of large, well-annotated datasets. To
address this issue, recent years have witnessed a growing emphasis on the
development of data-efficient deep learning methods. This paper conducts a
thorough review of data-efficient deep learning methods for medical image
analysis. To this end, we categorize these methods based on the level of
supervision they rely on, encompassing categories such as no supervision,
inexact supervision, incomplete supervision, inaccurate supervision, and only
limited supervision. We further divide these categories into finer
subcategories. For example, we categorize inexact supervision into multiple
instance learning and learning with weak annotations. Similarly, we categorize
incomplete supervision into semi-supervised learning, active learning, and
domain-adaptive learning and so on. Furthermore, we systematically summarize
commonly used datasets for data efficient deep learning in medical image
analysis and investigate future research directions to conclude this survey.Comment: Under Revie
Label-Free Liver Tumor Segmentation
We demonstrate that AI models can accurately segment liver tumors without the
need for manual annotation by using synthetic tumors in CT scans. Our synthetic
tumors have two intriguing advantages: (I) realistic in shape and texture,
which even medical professionals can confuse with real tumors; (II) effective
for training AI models, which can perform liver tumor segmentation similarly to
the model trained on real tumors -- this result is exciting because no existing
work, using synthetic tumors only, has thus far reached a similar or even close
performance to real tumors. This result also implies that manual efforts for
annotating tumors voxel by voxel (which took years to create) can be
significantly reduced in the future. Moreover, our synthetic tumors can
automatically generate many examples of small (or even tiny) synthetic tumors
and have the potential to improve the success rate of detecting small liver
tumors, which is critical for detecting the early stages of cancer. In addition
to enriching the training data, our synthesizing strategy also enables us to
rigorously assess the AI robustness.Comment: CVPR 202
Augmentation is AUtO-Net: Augmentation-Driven Contrastive Multiview Learning for Medical Image Segmentation
The utilisation of deep learning segmentation algorithms that learn complex
organs and tissue patterns and extract essential regions of interest from the
noisy background to improve the visual ability for medical image diagnosis has
achieved impressive results in Medical Image Computing (MIC). This thesis
focuses on retinal blood vessel segmentation tasks, providing an extensive
literature review of deep learning-based medical image segmentation approaches
while comparing the methodologies and empirical performances. The work also
examines the limitations of current state-of-the-art methods by pointing out
the two significant existing limitations: data size constraints and the
dependency on high computational resources. To address such problems, this work
proposes a novel efficient, simple multiview learning framework that
contrastively learns invariant vessel feature representation by comparing with
multiple augmented views by various transformations to overcome data shortage
and improve generalisation ability. Moreover, the hybrid network architecture
integrates the attention mechanism into a Convolutional Neural Network to
further capture complex continuous curvilinear vessel structures. The result
demonstrates the proposed method validated on the CHASE-DB1 dataset, attaining
the highest F1 score of 83.46% and the highest Intersection over Union (IOU)
score of 71.62% with UNet structure, surpassing existing benchmark UNet-based
methods by 1.95% and 2.8%, respectively. The combination of the metrics
indicates the model detects the vessel object accurately with a highly
coincidental location with the ground truth. Moreover, the proposed approach
could be trained within 30 minutes by consuming less than 3 GB GPU RAM, and
such characteristics support the efficient implementation for real-world
applications and deployments
Pixel-level semantic understanding of ophthalmic images and beyond
Computer-assisted semantic image understanding constitutes the substrate of applications that range from biomarker detection to intraoperative guidance or street scene understanding for self-driving systems. This PhD thesis is on the development of deep learning-based, pixel-level, semantic segmentation methods for medical and natural images. For vessel segmentation in OCT-A, a method comprising iterative refinement of the extracted vessel maps and an auxiliary loss function that penalizes structural inaccuracies, is proposed and tested on data captured from real clinical conditions comprising various pathological cases. Ultimately, the presented method enables the extraction of a detailed vessel map of the retina with potential applications to diagnostics or intraoperative localization. Furthermore, for scene segmentation in cataract surgery, the major challenge of class imbalance is identified among several factors. Subsequently, a method addressing it is proposed, achieving state-of-the-art performance on a challenging public dataset. Accurate semantic segmentation in this domain can be used to monitor interactions between tools and anatomical parts for intraoperative guidance and safety. Finally, this thesis proposes a novel contrastive learning framework for supervised semantic segmentation, that aims to improve the discriminative power of features in deep neural networks. The proposed approach leverages contrastive loss function applied both at multiple model layers and across them. Importantly, the proposed framework is easy to combine with various model architectures and is experimentally shown to significantly improve performance on both natural and medical domain
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