Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

2023 Abstracts

Development of a Quantum-Optimal Bioimaging System for Plant-Microbiome Interactions


Shaun Burd1, Joshua L. Reynolds1* ([email protected]), Tzu-Chieh Yen1, Adam Bowman1, Soichi Wakatsuki1,2, and Mark Kasevich1


1Stanford University; and 2SLAC National Accelerator Laboratory


  • Design and develop a quantum-information-optimal multi-pass (MP) microscope
  • Demonstrate MP stimulated Raman scattering microscopy for high-sensitivity, label-free chemical imaging
  • Develop technologies for quantum-optimal quantitative phase imaging and extend this approach towards interaction-free measurements
  • Apply artificial intelligence/machine learning methods to establish Raman signatures of different bacterial and fungal species in different environmental conditions
  • Apply the Raman MP microscope to follow plant-bacteria interactions during infections of isolated plant cells and tissues
  • Use the Raman MP microscope to elucidate how individual bacterial species interact with each other under a changing biofilm environment
  • Develop microfluidic devices coupled with Raman MP microscopy for efficient separation and concentration of soil bacteria into single species
  • Single cell geno- and phenotyping and cryo-electron tomography of purified cells


Researchers present progress towards the development of quantum-information-optimal multi-pass imaging technologies based on re-imaging optical systems (Juffmann et al. 2016). A multi-pass microscope interrogates a sample multiple times in a programmable and deterministic fashion. This leads to a metrological advantage for imaging weak scatterers. This enhanced sensitivity can yield a significant reduction in the damage imparted to the sample or can reduce image acquisition time. The approach can enter a quantum non-destructive regime where the photon interaction with the image target is fully coherent, and the imaging process becomes quantum non-destructive when conditioned upon the detection of single photons. Recent theoretical analysis has shown that this imaging approach saturates quantum information bounds and compares favorably with bounds obtained using squeezed and other entangled probe states, but avoids the technical complexity associated with the production of such states (Koppell and Kasevich 2022).

As proof-of-concept experiments, researchers will use these protocols for the study of microbe-microbe and microbe-plant interactions in multi-pass stimulated Raman microscopy (MP-SRS) configurations. These configurations will enable volumetric, chemically specific, imaging of thick samples. Furthermore, building on the demonstration of continuous-wave multi-pass flow cytometry (Israel et al. 2022), the Raman MP microscope will be integrated into extremely efficient, label-free microfluidic separators for isolating single species of soil bacteria. Researchers plan to design these quantum imaging technologies into compact and robust systems for shared use among the BER science community.


Juffmann, T., et 2016.Multi-Pass Microscopy.” Nature Communications 7, 12858.

Koppell, S. A., and M. A. Kasevich. 2022. “Optimal Dose-Limited Phase Estimation without Entanglement.” arXiv 2203, 10137.

Israel, Y., et al. 2022. “Continuous Wave Multi-Pass Imaging Flow Cytometry.” arXiv 2211, 15791.

Funding Information

This research was supported by the DOE Office of Science, Office of Biological and Environmental Research (BER), grant no. DE-SC0023076.