Typical Projects

Project Name Project Description Lead Faculty
Photo-thermal microscopy We propose to develop Photothermal Microscopy and Photothermal spectroscopy for label-free imaging and characterization of tissue and single cells. Our goal is to extend the rapidly evolving and exciting method for both wide-field imaging, and high-speed high-resolution microscopy. The microscope system is capable of chemical imaging using Vibrational infrared microscopy using Quantum Cascade Lasers, for deep tissue imaging in the near-infrared using coherent tunable laser sources, and even incoherent sources. Applications include imaging neural tissue associated with Traumatic Brain Injury (TBI) and Neurophotonics, as well novel applications to spectroscopy with Nanoplasmonic metamaterials. S. Erramilli
Adaptively compensated 3-D bio-imaging High-resolution three-dimensional (3D) imaging using multi-photon microscopy (MPM) in optically scattering biological tissue has become a critical and enabling tool for scientific discovery and bio-engineering advancement (1). While MPM offers inherent background rejection, its achievable image resolu-tion & imaging depth are limited by optical aberrations introduced by the tissue itself. Adaptive optics (AO) us-ing MEMS deformable mirrors (DMs) is possible, but challenging due to difficulty in measuring a wavefront through scattering media. We propose to use image-based AO feedback and open-loop DM control to double the effective resolution and achievable imaging depth in a two-photon microscope, adding less than 10% to system cost. T. Bifano
Label-free nanofluidic-nanoplasmonic biosensor Our aim is to demonstrate highly multiplexed, label-free, portable and rapid virus diagnostic technology that can be used by unskilled users to screen with minimal sample preparation large numbers of virus types that are relevant to global health. H. Altug
Light-controlled neuronal circuitry Recent developments in membrane biophysics, neurophysiology and molecular biology are providing the catalyst for the birth of a new technology termed neurophotonics. First envisioned by Francis Crick in 1979, neurophotonics provides a means to control and monitor individual nerves in complex neural circuits including the human brain using light. While the ultimate commercial impact of neuroophonics is still unclear, initial applications include restoring vision in the blind, controlling complex motor activity and treating brain disorders. In analogy with the growth of the computer industry driven by progress in semiconductor technology, future developments in neurophotonics depends on the design and bioengineering of optimized light activated proteins (LAPs) along with methods for targeting them to specific cells in a living organism. K. Rothschild
Rapid Diagnostics for UTI Worldwide, approximately 150 million people are diagnosed with urinary tract infections (UTIs) each year, costing over $6 billion and the increasing prevalence of drug resistant bacterial strains further creates the crucial need for the development of rapid, accurate novel diagnostic approaches. We will develop the use of surface enhanced Raman spectroscopy (SERS) to show that this optically based approach has the required bacterial concentration sensitivity and species/strain specificity to be used in clinical settings for the rapid (~30 min), reliable, easy-to-use, inexpensive diagnosis of bacterial pathogens in patients presenting with UTI symptoms. The successful development of this technology will lead to more accurate diagnosis of UTI and UTI-like presentations and better determinations of most appropriate narrow-spectrum antibiotic within the timeframe of a patients visit to a clinic/hospital, and help reduce microbial antibiotic resistance in the long term. L. Ziegler
Single-cell laser tweezers Raman spectroscopy The overall goal of this project is to develop a label-free single cell cytometry method that captures, and analyzes individual cells based on three foundations of technology: Raman spectroscopy, laser tweezers, and microfluidics. Raman spectroscopy enables label-free sensing and chemical analysis using the intrinsic molecular vibrational “fingerprints” of biomolecules like proteins, nucleic acids, and lipids. Laser tweezers allow for the selection and isolation of individual cells from their surrounding environment during the Raman analysis. Finally, the microfluidics technology allows for precise control of the cellular environment and the pre- and post-analysis processing of the cells. J. Chan
Monitoring Drug Dose Response of Single Cells Using Micro-Raman Spectroscopy The overall goal of this project is to apply single cell Raman spectroscopy/microscopy to study the drug response of single, living cells. Raman spectroscopy enables continuous, label-free chemical analysis and imaging of single cells as they interact with their local environment, which makes this technology ideally suited for monitoring cell-drug interactions. Raman signatures of cells can reflect the characteristic sub-cellular changes induced by chemotherapeutic drugs and be used to predict cell death via apoptosis. This technology has the potential to be developed into a compact, cost-effective analytical tool for testing patient response to drugs for treatment monitoring, drug screening and discovery, and microdose testing. J. Chan
Cell phone microscope and spectrometer for POC diagnosis This proposal aims to develop an inexpensive, simple and portable cell-phone-based prototype that includes a cell phone microscope and spectrometer for performing point of care or diagnosis such as determining a complete blood count (CBC) in rural and low resource settings. The blood analysis process will be enhanced and shortened by the ability of the device to transmit data and communicate with health care providers at a distant location. S. Wachsmann-Hoigu
Live cell superresolution microscopy The goal of this project is to extend the capabilities of a novel fluorescence microscopy technique for imaging samples beyond the optical diffraction limit utilizing three-dimensional structured illumination (3D-SIM) to enhance it’s utility for working with biological samples. Currently, the 3D-SIM system commercialized under the trade name DeltaVision|OMX by Applied Precision, Inc. is limited to work with fixed cells due to relatively slow image acquisition times. Also the resolution is limited to 100nm in the x-y plane and 200nm in the z plane. T. Huser
Direct molecular detection via SERS and aptamers Detection and tracking of molecules is invaluable not only in the field of medical diagnostics but also in drug development and analysis, environmental monitoring, forensic investigations and biodefense. Most commonly used methods make use of fluorescent labels as probe molecules. Labeling of biomolecules is not always advantageous at it can render the biomolecules inactive. In addition, these probes are susceptible to photobleaching. The proposed study aims to develop a label free assay for direct detection of biomolecules using aptamers as molecular receptors and Surface Enhanced Raman Spectroscopy (SERS) as detection method. The technique takes advantage of the sensitivity of SERS (shown to be able to measure signal from single molecules)1 as well as the stability and the compact secondary structure of the aptamer. The technique is specific, robust, cost effective, and greatly reduces the amount of time normally involved in sandwich type assays. S. Wachsmann-Hogiu
Optical Coherence Tomography non-invasive 3-D imaging of tissue morphology & blood perfusion The overall goal of this project is to develop high speed (>100k A-line/s) and high resolution (<3µm) Optical Coherence Tomography system for imaging tissue samples. Optical Coherence Tomography is imaging modality that allows rapid 3D mapping of tissue morphology, based on intensity of back scattered light. It implements coherent detection scheme were the reference light is interfered with the sample signal resulting in very high sensitivity (~110dB). The proposed functional extension of OCT allows detection of the motion within the sample by monitoring phase variation in the detected signal. We originally developed this technology to monitor blood flow in the retina of the living human eye and are now planning to extend it beyond ophthalmic imaging. R. Zawadzki
Adaptive-optics enhanced multi-modal imaging systems The overall goal of this project is to develop Adaptive Optics enhanced multimodal imaging system that combines Optical Coherence Tomography with confocal microscopy for imaging biological samples. Adaptive Optics allows measurement and correction of the optical aberrations of the imaged sample and imaging system itself to allow diffraction limited imaging resulting in high resolution and increased signal. Multimodal imaging systems allow simultaneous acquisition of the sample data sets using different optical signals. This allows creation of co-registered tissue maps. Optical Coherence Tomography is imaging modality that allows rapid 3D mapping of tissue morphology, based on intensity of back scattered light. Confocal Microscopy is “classical” imaging modality that uses confocal pinhole to reject out of focus light to increase axial and lateral resolution of the system; it can be used in many configurations including measuring linear as well as nonlinear optical effects. R. Zawadzki
Atomic-resolution dynamic imaging of membrane proteins using XFEL’s This project will develop advanced sample platform techniques that will enable atomic-resolution imaging of membrane proteins using the ultra-bright x-ray pulses from hard x-ray free electron lasers (XFELs), such as LCLS at SLAC/Stanford. First proof of concept experiments (as published in Nature, Feb 3, 2011) demonstrated that x-ray diffraction imaging of biomolecules at XFELs can provide high-resolution structural information. Major bottlenecks, in particular in the area of efficient sample introduction and image reconstruction, remain before this method will be more practical for imaging a wide range of membrane proteins (with still unknown structures) and their interactions with other molecules (e.g., toxins or drugs). This project will leverage ongoing UC Davis efforts on XFEL bioimaging (funded by UC; in collaboration with LLNL). The proposed budget is for a new dedicated postdoc and some hardware. M. Coleman