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Cell segmentation from wide-field light microscopy images using CNNs
GHAZNAVI, Ali
Image object segmentation allows localising the region of interest in the image (ROI) and separating the foreground from the background. Cell detection and segmentation are the primary and critical steps in microscopy image analysis. Analysing microscopy images allows us to extract vital information about the cells, including their morphology, size, and life cycle. On the other hand, living cell segmentation is challenging due to the complexity of these datasets. This research focused on developing Artificial Intelligence/Machine Learning methods of single- and multi-class segmentation of living cells. For this study, the Negroid cervical epithelioid carcinoma HeLa line was chosen as the oldest, immortal, and most widely used model cell line. Several time-lapse image series of living HeLa cells were captured using a high-resolved wide-field transmitted/reflected light microscope (custom-made for the Institute of Complex System, Nové Hrady, Czech Republic) to observe micro-objects and cells. Employing a telecentric objective with a high-resolution camera with a large sensor size allows us to achieve a high level of detail and sharper borders in large microscopy images. The collected time-lapse images were calibrated and denoised in the pre-processing step. The data sets collected under the transmission microscope setup were analyzed using a simple U-Net, Attention U-Net, and Residual Attention U-Net to achieve the best single-class semantic segmentation result. The data sets collected under the reflection microscope setup were analyzed using hybrid U-Net methods, including Vgg19-Unet, Inception-Unet, and ResNet34-Unet, to achieve the most precise multi-class segmentation result.
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Semantic segmentation using support vector machine classifier
Pecha, Marek ; Langford, Z. ; Horák, David ; Tran Mills, R.
This paper deals with wildfire identification in the Alaska regions as a semantic segmentation task using support vector machine classifiers. Instead of colour information represented by means of BGR channels, we proceed with a normalized reflectance over 152 days so that such time series is assigned to each pixel. We compare models associated with $\mathcal{l}1$-loss and $\mathcal{l}2$-loss functions and stopping criteria based on a projected gradient and duality gap in the presented benchmarks.
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Assessment of Uncertainty of Neural Net Predictions in the Tasks of Classification, Detection and Segmentation
Vlasák, Jiří ; Kohút, Jan (referee) ; Herout, Adam (advisor)
This work focuses on comparing three widely used methods for improving uncertainty estimations: Deep Ensembles, Monte Carlo Dropout, and Temperature Scaling. These methods are applied to six computer vision models that are pretrained as well as trained from scratch. The models are then evaluated on computer vision datasets for classification, semantic segmentation, and object detection using a wide range of metrics. The models are also evaluated on distorted versions of these datasets to measure their performance on out-of-distribution data. These modified models achieve promising results. Ensembles outperform the other models by as high as 70 % in accuracy and 0.2 in IOU on the distorted MedSeg COVID-19 segmentation dataset while also outperforming the other models on the CIFAR-100 and FMNIST datasets.
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Predicting Trajectories of Vehicles and Pedestrians for Driving Assistent Systems
Mudroň, Marek ; Musil, Petr (referee) ; Smrž, Pavel (advisor)
This bachelor thesis deals with representation of a traffic scene by processing monocular video sequence. I try to predict a trajectory of detected vehicles in a short time horizon, based on created representation. Current approaches use multiple expensive sensors to gather instant information of environment. In the thesis I introduce technique, which is able to extract data from an environment by image processing techniques without the need of expensive sensors. The result of this work is a system creating opportunity to reduce the sensor costs of a system for scene representation and trajectory prediction of vehicles in the scene. In addition, comparison of models trained on differently processed data is provided, as well as data about how my system approximates the most reliable prediction models.
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Object Detection in the Laser Scans Using Convolutional Neural Networks
Marko, Peter ; Beran, Vítězslav (referee) ; Veľas, Martin (advisor)
This thesis is aimed at detection of lines of horizontal road markings from a point cloud, which was obtained using mobile laser mapping. The system works interactively in cooperation with user, which marks the beginning of the traffic line. The program gradually detects the remaining parts of the traffic line and creates its vector representation. Initially, a point cloud is projected into a horizontal plane, crating a 2D image that is segmented by a U-Net convolutional neural network. Segmentation marks one traffic line. Segmentation is converted to a polyline, which can be used in a geo-information system. During testing, the U-Net achieved a segmentation accuracy of 98.8\%, a specificity of 99.5\% and a sensitivity of 72.9\%. The estimated polyline reached an average deviation of 1.8cm.
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Urban Element Detection Using Satellite Imagery
Oravec, Dávid ; Herout, Adam (referee) ; Zlámal, Adam (advisor)
Táto práca sa zameriava na správnu detekciu objektov v satelitných snímkach pomocou konvolučných neuronových sietí. Cieľom práce je pomocou natrénovaného modelu detekovať bazény a tenisové ihriská v satelitných snímkach z rôznych miest. Model pracuje s dátami z 10 rôznych miest. Pri vypracovaní bol využitý model neurónovej siete RetinaNet a knižnica Detectron2. Model, ktorý sa podarilo vytrénovať, dokáže detekovať objekty s priemernou presnosťou (AP50) na úrovni 63,402 %. Práca môže byť prínosom v oblasti automatizovania získavania štatistík o povrchu zeme.
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Self-supervised learning in computer vision applications
Vančo, Timotej ; Richter, Miloslav (referee) ; Janáková, Ilona (advisor)
The aim of the diploma thesis is to make research of the self-supervised learning in computer vision applications, then to choose a suitable test task with an extensive data set, apply self-supervised methods and evaluate. The theoretical part of the work is focused on the description of methods in computer vision, a detailed description of neural and convolution networks and an extensive explanation and division of self-supervised methods. Conclusion of the theoretical part is devoted to practical applications of the Self-supervised methods in practice. The practical part of the diploma thesis deals with the description of the creation of code for working with datasets and the application of the SSL methods Rotation, SimCLR, MoCo and BYOL in the role of classification and semantic segmentation. Each application of the method is explained in detail and evaluated for various parameters on the large STL10 dataset. Subsequently, the success of the methods is evaluated for different datasets and the limiting conditions in the classification task are named. The practical part concludes with the application of SSL methods for pre-training the encoder in the application of semantic segmentation with the Cityscapes dataset.
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Semantic segmentation of images using convolutional neural networks
Špila, Filip ; Věchet, Stanislav (referee) ; Krejsa, Jiří (advisor)
Tato práce se zabývá rešerší a implementací vybraných architektur konvolučních neuronových sítí pro segmentaci obrazu. V první části jsou shrnuty základní pojmy z teorie neuronových sítí. Tato část také představuje silné stránky konvolučních sítí v oblasti rozpoznávání obrazových dat. Teoretická část je uzavřena rešerší zaměřenou na konkrétní architekturu používanou na segmentaci scén. Implementace této architektury a jejích variant v Caffe je převzata a upravena pro konkrétní použití v praktické části práce. Nedílnou součástí tohoto procesu jsou kroky potřebné ke správnému nastavení softwarového a hardwarového prostředí. Příslušná kapitola proto poskytuje přesný návod, který ocení zejména noví uživatelé Linuxu. Pro trénování všech variant vybrané sítě je vytvořen vlastní dataset obsahující 2600 obrázků. Je také provedeno několik nastavení původní implementace, zvláště pro účely použití předtrénovaných parametrů. Trénování zahrnuje výběr hyperparametrů, jakými jsou například typ optimalizačního algoritmu a rychlost učení. Na závěr je provedeno vyhodnocení výkonu a výpočtové náročnosti všech natrénovaných sítí na testovacím datasetu.
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A convolutional neural network for image segmentation
Mitrenga, Michal ; Petyovský, Petr (referee) ; Jirsík, Václav (advisor)
The aim of the bachelor thesis is to learn more about the problem of convolutional neural networks and to realize image segmentation. This theme includes the field of computer vision, which is used in systems of artificial intelligence. Special Attention is paid to the image segmentation process. Furthermore, the thesis deals with the basic principles of artificial neural networks, the structure of convolutional neural networks and especially with the description of individual semantic segmentation architectures. The chosen SegNet architecture is used in a practical application along with a pre-learned network. Part of the work is a database of CamVid images, which is used for training. For testing, a custom image database is created. Practical part is focused on CNN training and searching for unsuitable parameters for network learning using SW Matlab.
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