High-Throughput Microscopy of E. coli Cells with Micropatterned Agarose Devices

Key to creating robust synthetic circuits are methods to evaluate their performance. Due to the inherent noisiness of biological systems, single cell methods, such as microscopy, are preferred since large populations of cells can be accurately quantitated, and growth of individual microcolonies can be tracked over time. The method of choice for imaging bacterial cells is to sandwich them between a thin layer of agarose gel and a coverslip. However a significant drawback of this method is that cells form clumps, which hinders automatic cell segmentation during image analysis. To solve this problem, we developed a method for physical segregation of cells by imprinting micro-patterned features onto the gel surface. By arraying the micro-patterning, we created a large-format agarose pad system, called Capsule Hotel, that can image 1000s of cells at 24 samples per pad. We also created a live cell version that allows time-lapse imaging of 10s of micro-colonies, at 24 samples per pad. We applied this system to study sources of gene expression noise in E. coli. Capsule Hotel is an easy to use, versatile microscopy system broadly applicable to systems and synthetic biology of microbes.