Cell segmentation from telecentric bright-field transmitted light microscopy images using a Residual Attention U-Net: a case study on HeLa line

• Published in: arXiv.org
• Main Authors: Ghaznavi, Ali, Rychtarikova, Renata, Saberioon, Mohammadmehdi, Stys, Dalibor
• Format: Paper Journal Article
• Language: English
• Published: Ithaca Cornell University Library, arXiv.org 06.07.2022
• Subjects: Cells (biology); Computer Science - Computer Vision and Pattern Recognition; Datasets; Deep learning; Image segmentation; Image transmission; Optical microscopy; Quantitative Biology - Quantitative Methods; Semantic segmentation; Semantics
• ISSN: 2331-8422
• DOI: 10.48550/arxiv.2203.12290

Living cell segmentation from bright-field light microscopy images is challenging due to the image complexity and temporal changes in the living cells. Recently developed deep learning (DL)-based methods became popular in medical and microscopy image segmentation tasks due to their success and promising outcomes. The main objective of this paper is to develop a deep learning, U-Net-based method to segment the living cells of the HeLa line in bright-field transmitted light microscopy. To find the most suitable architecture for our datasets, a residual attention U-Net was proposed and compared with an attention and a simple U-Net architecture. The attention mechanism highlights the remarkable features and suppresses activations in the irrelevant image regions. The residual mechanism overcomes with vanishing gradient problem. The Mean-IoU score for our datasets reaches 0.9505, 0.9524, and 0.9530 for the simple, attention, and residual attention U-Net, respectively. The most accurate semantic segmentation results was achieved in the Mean-IoU and Dice metrics by applying the residual and attention mechanisms together. The watershed method applied to this best -- Residual Attention -- semantic segmentation result gave the segmentation with the specific information for each cell.