Image Preprocessing Pipeline for Bright-Field Miniature Live Cell Microscopy Prototypes

Abstract

One of the biggest technical challenges in live cell imaging is to keep the cells in a healthy state while imaging them. In fact, being able to observe living cells in their cultivation environment over time is a major step to understand and diagnose diseases. For this purpose, we are using a novel microscopic system composed of microscopy prototypes that can, in contrast to most available live cell microscopes, operate in an incubator. Each prototype observes one well of a 24 well plate over time. The in-incubator operability imposes manufacturing constraints on the size of our microscopic system and consequently degrades the delivered image quality. In order to get usable live cell images with the prototypes, a preprocessing pipeline was introduced. First, the exposure time is increased until the circular illumination is visible. Second, the illumination field is estimated using Gaussian smoothing and the center of the circular illumination is detected. Third, based on the illumination center, a 1 mm$^{2}$ region is cropped. Fourth, using the resulting image’s standard deviation, a suitable exposure time is found in order to avoid under- or over-exposure. Finally, the illumination is corrected by subtracting the estimated illumination field and the image contrast is stretched. The prototypes and the pipeline are currently in use at the laboratory of our bioprocess engineering partners. The generated images and videos enable them to analyse the behavior of cells over time.