corona discharge gun, Shinko Denso).

This assemblage is then once again exposed to air plasma (, corona discharge gun), covered with a solution of polyethylene glycol-poly-L-lysine (PEG-PLL, Nanocs, PG2k-PLY), and left to rest for 30 minutes. Ungrafted PEG-PLL is then washed away with deionized water. PDMS microwells and glass cover slide are now treated hydrophilic, and PEG-PLL coating prevents non-specific adhesion of bacteria. Finally, the flow cell is completed with the glass cover slip (untreated) being attached to the glass cover slide with the adhesive spacer placed over the unpatterned areas of the PDMS sheet. It is used immediately after fabrication (Fig. \[fig.s1\] Step 1).

![**Schematic illustration of device fabrication.** Step 1: device construction. A thin PDMS layer patterned with microwells is transferred between the two glass slides of a flow cell and coated with PEG-PLL to avoid unspecific adhesion of bacteria. Step 2: bacterial suspension is injected from one side of the flow cell. Step 3: excess bacterial suspension is flushed out by a mixture of oil and surfactant. This mixture seals the microwells on their top side. Step 4: device is sealed at both ends with epoxy glue.[]{data-label="fig.s1"}](figureS1_3.jpg)

Filling protocol
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Once a flow cell is ready, it 