Fig. 1

Microfluidic bacterial culture setup and analysis empowers long-term analysis of Synechocystis growth and division. a Cross-section of the microfluidic cell culture chip. Top flow layer contains cyanobacterial cells. Flow can be controlled using push-up valves. Setup was modified to enable automated control of LED illumination. Gases, including CO₂, can diffuse into the cell culture chambers. b Imaging analysis pipeline, in which the original image (1) is first segmented into a binary image (2), from which cell clusters are identified (3), and then further segmented into single cells whenever possible (4). For each single cell identified in a cluster, the contour defining the interior and the location of the center are determined. Scale bar: 5 μm. c Each gray line represents the growth trajectory of one Synechocystis lineage starting from a single cell, normalized to the initial cell volume. The mean normalized growth (black) and standard deviation (shaded orange) are shown. Total cell number (blue) based on the automated image analysis pipeline in (b) increases at the same rate as total lineage volume for the first 40 h. d Residuals from exponential fits of individual lineage growth curves (gray) during the first 12 h of growth (top) and between 29 and 41 h (bottom) exhibited small root mean square error (RMSE), demonstrating exponential growth. The mean of all residuals is shown in black