NOVEL MODEL-BASED AND DEEP LEARNING APPROACHES TO SEGMENTATION AND OBJECT DETECTION IN 3D MICROSCOPY IMAGES

Modeling microscopy images and extracting information from them are important problems in the fields of physics and material science.

Model-based methods, such as marked point processes (MPPs), and machine learning approaches, such as convolutional neural networks (CNNs), are powerful tools to perform these tasks. Nevertheless, MPPs present limitations when modeling objects with irregular boundaries. Similarly, machine learning techniques show drawbacks when differentiating clustered objects in volumetric datasets.

In this thesis we explore the extension of the MPP framework to detect irregularly shaped objects. In addition, we develop a CNN approach to perform efficient 3D object detection. Finally, we propose a CNN approach together with geometric regularization to provide robustness in object detection across different datasets.

The first part of this thesis explores the addition of boundary energy to the MPP by using active contours energy and level sets energy. Our results show this extension allows the MPP framework to detect material porosity in CT microscopy images and to detect red blood cells in DIC microscopy images.

The second part of this thesis proposes a convolutional neural network approach to perform 3D object detection by regressing objects voxels into clusters. Comparisons with leading methods demonstrate a significant speed-up in 3D fiber and porosity detection in composite polymers while preserving detection accuracy.

The third part of this thesis explores an improvement in the 3D object detection approach by regressing pixels into their instance centers and using geometric regularization. This improvement demonstrates robustness when comparing 3D fiber detection in several large volumetric datasets.

These methods can contribute to fast and correct structural characterization of large volumetric datasets, which could potentially lead to the development of novel materials.