Microscopic image segmentation (MIS) is a fundamental task in medical imaging and biological research, essential for precise analysis of cellular structures and tissues. Despite its importance, the segmentation process encounters significant challenges, including variability in imaging conditions, complex biological structures, and artefacts (e.g., noise), which can compromise the accuracy of traditional methods. The emergence of deep learning (DL) has catalyzed substantial advancements in addressing these issues. This systematic literature review (SLR) provides a comprehensive overview of state-of-the-art DL methods developed over the past six years for the segmentation of microscopic images. We critically analyze key contributions, emphasizing how these methods specifically tackle challenges in cell, nucleus, and tissue segmentation. Additionally, we evaluate the datasets and performance metrics employed in these studies. By synthesizing current advancements and identifying gaps in existing approaches, this review not only highlights the transformative potential of DL in enhancing diagnostic accuracy and research efficiency but also suggests directions for future research. The findings of this study have significant implications for improving methodologies in medical and biological applications, ultimately fostering better patient outcomes and advancing scientific understanding.

Microscopic image segmentation (MIS) plays a pivotal role in various fields such as medical imaging and biology. With the advent of deep learning (DL), numerous methods have emerged for automating and improving the accuracy of this crucial image analysis task. This systematic literature review (SLR) aims to provide an exhaustive overview of the state-of-the-art DL methods employed for the segmentation of microscopic images. In this review, we analyze a diverse array of studies published in the last five years, highlighting their contributions, methodologies, datasets, and performance evaluations. We explore the evolution of DL techniques and their adaptation to specific segmentation challenges, from cell and nucleus segmentation to tissue analysis. This paper, through the integration of existing knowledge, provides valuable perspectives for researchers involved in the field of microscopic image segmentation.