Ultrasound image segmentation thesis

Ultrasound image segmentation thesis

This bachelor’s thesis deals with basic description of ultrasonography, principles of contrast-enhanced imaging and application of segmentation methods in ultrasound problematics. Some individual methods were implemented in Matlab, version Rb Ultrasound Image Segmentation Chitresh Bhushan April 15, 1 Introduction Ultrasound imaging or ultrasonography is an important diagnosis method in medical analysis. It is important to segment out cavities, di erent types of tissues and organs in the ultrasound image for e ective and correct diagnosis. Human experts are very good Automatic segmentation of prostate in TRUS images using modified V-net convolutional neural network. This is the final fully commented version of the code used in my master thesis "Automatic prostate segmentation in transrectal ultrasound images using modified V-net convolutional neural network" [].The repository contains all scripts for complete analysis, which are organized into 5 logical

Ultrasound image segmentation thesis

Python workflow for automatic prostate segmentation in transrectal ultrasound 3d images by using deep learning v-net model. This is the final fully commented version of the code used in my master thesis "Automatic prostate segmentation in transrectal ultrasound images using modified V-net convolutional neural network" [ Full text ].

The repository contains all scripts for complete analysis, which are organized into 5 logical modules. Often, the original medical images have very high resolution and might be heavy on system resources. To ultrasound image segmentation thesis this issue different ultrasound image segmentation thesis methods are utilized, such as cropping of the region of interest, rescaling, and normalization.

Augmentation is an essential step when working with a limited sample size. The scripts include a collection of numpy and scipy functions, as well as a function for probabilistic augmentation used for hyperparameter optimization. This function generate augmented images on the fly during the hyperparameter optimization, while the frequency of each type of augmentation can be specified when calling the function. Training a robust model requires a lot of time.

To reduce the time needed for a search for an optimal model, hyperparameter optimization ultrasound image segmentation thesis introduced. The hyperparameter optimization script is built upon Keras Tuner. A custom tuner has been implemented that search for the best augmentation methods and parameters, a dynamic V-net model choosing between different loss functions and different model depth. By using a Data manager data. py the preprocessed data is read and piped into the fit function.

During the training session, various metrics are measured and saved, namely loss, accuracy, and Sørensen—Dice. Testing uses a saved model to predict the prostate structure on preprocessed test images as a 3D binary mask. For preprocessing of the test images the same preprocessing steps and scripts are used. The initial prediction might contain false positives, thus we introduced the postprocessing step. In this step, the images are analyzed layer by layer and on each layer, only the largest structure is saved.

This significantly reduces the number of false positives and improves metrics as Hausdorf distance and Average surface distance. For the analysis, two types of models were used, based on the V-net model, a four-level and a five-level V-net neural network. Additionally, there is a dynamic model which has several hyperparameters and it is intended to be used for hyperparameter optimization.

Images and binary mask should have same name. The workflow has been tested using a specific size of images.

The scripts work with a different resolution as well, but they should be modified accordingly beforehand. Skip to content. MIT License. Code Issues Pull requests Actions Projects Wiki Security Insights.

Branches Tags. Could not load branches. Could not ultrasound image segmentation thesis tags. Latest commit. Git stats 40 commits. Failed to load latest commit information. View code. Automatic segmentation of prostate in TRUS images using modified V-net convolutional neural network Preprocessing preprocessing. py, augment. py Post-processing postprocessing. py Metrics metrics. py Models V-net 4 lvl model V-net 5 lvl model Requirements Quick start Examples: Preprocessing preprocessing.

py Postprocessing postprocessing. Automatic segmentation of prostate in TRUS images using modified V-net convolutional neural network This is the final fully commented version of the code used in my master thesis "Automatic prostate segmentation in transrectal ultrasound images using modified V-net convolutional neural network" [ Full text ].

Preprocessing preprocessing. py Preprocessing Often, the original medical images have very high resolution and might be heavy on system resources. Augmentation Augmentation is an essential step when working with a limited sample size. py Training a robust model requires a lot of time. py By using a Data manager data. Post-processing postprocessing. py The initial prediction might contain false positives, thus we introduced the postprocessing step.

Metrics metrics. py Measures Dice score, Jaccard score, Hausdorf, ultrasound image segmentation thesis, Average Surface Distance, ultrasound image segmentation thesis. Models For the analysis, ultrasound image segmentation thesis, two types of models were used, based on the V-net model, a four-level and a five-level V-net neural network, ultrasound image segmentation thesis.

About Python workflow for automatic prostate segmentation in transrectal ultrasound 3d images by using deep learning v-net model. Topics python deep-learning tensorflow keras image-processing segmentation 3d. Releases No releases published. Packages 0 No packages published. Terms Privacy Security Status Docs Contact GitHub Pricing API Training Blog About. You signed ultrasound image segmentation thesis with another tab or window.

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A thesis submitted in fulfilment of the ultrasound images into three different groups namely normal, infectious and cystic Image Segmentation 34 Vector Graphic Image 37 Automatic Kidney Region of Interest Generation 41 Feature Extraction of Kidney US Images 42 Automatic segmentation of prostate in TRUS images using modified V-net convolutional neural network. This is the final fully commented version of the code used in my master thesis "Automatic prostate segmentation in transrectal ultrasound images using modified V-net convolutional neural network" [].The repository contains all scripts for complete analysis, which are organized into 5 logical MASTER THESIS Automatic localisation and segmentation of the Left Ventricle in Cardiac Ultrasound Images Presented by: Esther PUYOL IG 3A F4B and MR 2A SISEA / Supervisor: Paolo PIRO Academic supervisor: Guy CAZUGUEL Company: MEDISYS - PHILIPS RESEARCH PARIS University: TELECOM BRETAGNE 17th March - 12th September