csPWS-seg

Deep-learning-driven automatic nuclei segmentation for chromatin-sensitive partial wave spectroscopic (csPWS) microscopy

Chromatin-sensitive partial wave spectroscopic (csPWS) microscopy, a novel spectroscopic nanosensing technique, offers a noninvasive glimpse into the mass density distribution of cellular structures at the nanoscale, allowing the analysis of chromatin structure and organization and the global transcriptional state of the cell nuclei for the study of its role in carcinogenesis. Accurate segmentation of the nuclei in csPWS microscopy images is an essential step in isolating them for further analysis. Existing manual segmentation is error-prone, biased, time-consuming, and laborious, resulting in disrupted nuclear boundaries with partial or over-segmentation. We developed a deep-learning-based automatic nuclei segmentation algorithm called csPWS-seg for live cell images captured using csPWS microscopy. The automatic and accurate nuclei segmentation offered by the csPWS-seg enhances the reliability of chromatin analysis research, paving the way for more accurate diagnostics, treatment, and understanding of cellular mechanisms for cancer.

• GitHub code Page: Gaire Laboratory GitHub page. 

Related Publications:

• Md. Shahin Alom et al., "Automatic nuclei segmentation of label-free chromatin-sensitive partial wave spectroscopic microscopy using convolution neural network with transformer." Proceedings Volume 13331, Label-free Biomedical Imaging and Sensing (LBIS) 2025; 1333102 (2025).

• Md. Shahin Alom, Ali Daneshkhah, Nicolas Acosta, Nick Anthony, Emily Pujadas Liwag, Vadim Backman and Sunil Kumar Gaire, "Deep Learning-driven Automatic Nuclei Segmentation of Live Cell Chromatin-sensitive Partial Wave Spectroscopic Microscopy Imaging," Optics Express, 32 (25), pp. 45052-45074 (2024). 

•  Md. Shahin Alom, Ali Daneshkhah, Nicolas Acosta, Nick Anthony, Emily Pujadas Liwag, Vadim Backman and Sunil Kumar Gaire, "Deep Learning-driven Automatic Nuclei Segmentation of Label-free Live Cell Chromatin-sensitive Partial Wave Spectroscopic Microscopy Imaging," bioRxiv (20 Aug 2024).