Label-free Monitoring of Nucleoid Dynamics of Bacteria for Drug Screening Using Holography

Abstract

We introduce holographic microscopy (HM) as a compact, low-cost, label-free, non-specific alternative to fluorescence microscopy (FM) for quantifying bacterial physiological responses during drug screening. Using the regularized inverse holographic volumetric reconstruction (RIHVR) framework, we extract phase maps from HM images and then invert the reconstructed phase to generate fluorescence-like contrast, in which bright inverted-phase regions correspond to bacterial nucleoid content captured by FM signals. We show that this relationship holds across multiple bacterial species, growth stages, drug treatments, and post-treatment time points, demonstrating that HM can consistently capture nucleoid associated structural information without fluorescent labeling. Because HM phase images contain both whole-cell refractive-index information and internal nucleoid-associated contrast, they enable simultaneous quantification of cell boundaries, cell length, nucleoid size, and nucleoid occupancy. These measurements allow drug-induced changes in bacterial morphology and nucleoid organization to be monitored over time. Unlike FM, which can suffer from photobleaching and may perturb live cells through phototoxicity, HM relies on refractive-index variations and maintains stable signal quality for long-term live-cell imaging. By linking label-free phase imaging to nucleoid-scale physiological readouts, this work establishes a path toward automated, high-throughput, and experimentally simpler bacterial drug-screening assays.