Understanding the Phase Contrast Optics to Restore Artifact-Free Microscopy Images for Segmentation


Phase contrast, a noninvasive microscopy imaging technique, is widely used to capture time-lapse images to monitor the behavior of transparent cells without staining or altering them. Due to the optical principle, phase contrast microscopy images contain artifacts such as the halo and shade-off that hinder image segmentation, a critical step in automated microscopy image analysis. Rather than treating phase contrast microscopy images as general natural images and applying generic image processing techniques on them, we propose to study the optical properties of the phase contrast microscope to model its image formation process. The phase contrast imaging system can be approximated by a linear imaging model. Based on this model and input image properties, we formulate a regularized quadratic cost function to restore artifact-free phase contrast images that directly correspond to the specimen's optical path length. With artifacts removed, high quality segmentation can be achieved by simply thresholding the restored images. The imaging model and restoration method are quantitatively evaluated on microscopy image sequences with thousands of cells captured over several days. We also demonstrate that accurate restoration lays the foundation for high performance in cell detection and tracking.


Computer Science

Keywords and Phrases

Automated Microscopy; Cell Detection; Critical Steps; Generic Images; High-Quality Segmentation; Image Formation Process; Imaging Model; Input Image; Linear Imaging; Microscopy Images; Microscopy Imaging; Natural Images; Optical Path Lengths; Phase Contrast Microscopes; Phase Contrasts; Phase-Contrast Image; Phase-Contrast Imaging; Phase-Contrast Microscopy; Quadratic Cost Functions; Restoration Methods; Thresholding; Time Lapse Images; Image Analysis; Image Reconstruction; Imaging Techniques; Optical Data Processing; Optical Properties; Restoration; Image Segmentation; Accuracy; Article; Artifact; Cell Density; Cell Tracking; Halo Effect; Image Processing; Image Quality; Imaging System; Optic Tract; Optics; Phase Contrast Microscope; Phase Contrast Microscopy; Phase Contrast Optics; Priority Journal; Quantitative Analysis; Artifacts; Cell Tracking; Computer Simulation; Computer-Aided Design; Equipment Design; Equipment Failure Analysis; Lenses; Microscopy; Phase-contrast; Models; Theoretical; Reproducibility of Results; Sensitivity and Specificity; Subtraction Technique; Image Restoration; imaging Model; Microscopy Image Analysis; Phase Contrast Optics

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Article - Journal

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