Unraveling Complexity: Panoptic Segmentation in Cellular and Space Imagery

Abstract

Advancements in machine learning, especially deep learning, have facilitated the creation of models capable of performing tasks previously thought impossible. This progress has opened new possibilities across diverse fields such as medical imaging and remote sensing. However, the performance of these models relies heavily on the availability of extensive labeled datasets. Collecting large amounts of labeled data poses a significant financial burden, particularly in specialized fields like medical imaging and remote sensing, where annotation requires expert knowledge. To address this challenge, various methods have been developed to mitigate the necessity for labeled data or leverage information contained in unlabeled data. These encompass include self-supervised learning, few-shot learning, and semi-supervised learning. This dissertation centers on the application of semi-supervised learning in segmentation tasks. We focus on panoptic segmentation, a task that combines semantic segmentation (assigning a class to each pixel) and instance segmentation (grouping pixels into different object instances). We choose two segmentation tasks in different domains: nerve segmentation in microscopic imaging and hyperspectral segmentation in satellite images from Mars. Our study reveals that, while direct application of methods developed for natural images may yield low performance, targeted modifications or the development of robust models can provide satisfactory results, thereby unlocking new applications like machine-assisted annotation of new data. This dissertation begins with a challenging panoptic segmentation problem in microscopic imaging, systematically exploring model architectures to improve generalization. Subsequently, it investigates how semi-supervised learning may mitigate the need for annotated data. It then moves to hyperspectral imaging, introducing a Hierarchical Bayesian model (HBM) to robustly classify single pixels. Key contributions of include developing a state-of-the-art U-Net model for nerve segmentation, improving the model's ability to segment different cellular structures, evaluating semi-supervised learning methods in the same setting, and proposing HBM for hyperspectral segmentation. The dissertation also provides a dataset of labeled CRISM pixels and mineral detections, and a software toolbox implementing the full HBM pipeline, to facilitate the development of new models.