Microscopy image analysis is a major bottleneck in quantification of single-cell microscopy data, typically requiring human oversight and curation, which limit both accuracy throughput. To address this, we developed deep learning-based pipeline that performs segmentation, tracking, lineage reconstruction. Our focuses on time-lapse movies Escherichia coli cells trapped "mother machine" microfluidic device, scalable platform for long-term widely used the field. While learning has been applied...

Flow cytometry is one of the most important technologies for high-throughput single-cell analysis. Fluorescent labeling acts as primary approach cellular analysis in flow cytometry. Nevertheless, fluorescent tags are not applicable to all cases, especially small molecules, which may significantly perturb biological functionality. Spontaneous Raman scattering offers capability non-invasively detect chemical contents cells but suffers from slow data acquisition. In order achieve label-free...

Label-free vibrational imaging by stimulated Raman scattering (SRS) provides unprecedented insight into real-time chemical distributions in living systems. Specifically, SRS the fingerprint region can resolve multiple chemicals a complex bio-environment using specific and well-separated signatures. Yet, with microsecond spectral acquisition has not been achieved due to small cross-sections lack of ultrafast scheme high resolution fidelity. Here, we report spectroscopic platform that acquires...

Abstract Coherent Raman scattering (CRS) microscopy is a chemical imaging modality that provides contrast based on intrinsic biomolecular vibrations. To date, endeavors instrumentation have advanced CRS into powerful analytical tool for studies of cell functions and in situ clinical diagnosis. Nevertheless, the small cross-section sets up physical boundary design space system, which trades off speed, signal fidelity spectral bandwidth. The synergistic combination computational approaches...

Stimulated Raman scattering (SRS) microscopy has shown enormous potential in revealing molecular structures, dynamics, and couplings complex systems. However, the sensitivity of SRS is fundamentally limited to millimolar level due shot noise small modulation depth. To overcome this barrier, we revisit from perspective energy deposition. The process pumps molecules their vibrationally excited states. subsequent relaxation heats up surroundings induces refractive index changes. By probing...

Abstract Spectroscopic stimulated Raman scattering (SRS) imaging generates chemical maps of intrinsic molecules, with no need for prior knowledge. Despite great advances in instrumentation, the acquisition speed a spectroscopic SRS image stack is fundamentally bounded by pixel integration time. In this work, we report three-dimensional sparsely sampled that measures ~20% pixels throughout stack. conjunction related work low-rank matrix completion (e.g., Netflix Prize), develop regularized...

Hyperspectral stimulated Raman scattering (SRS) by spectral focusing can generate label-free chemical images through temporal scanning of chirped femtosecond pulses. Yet, pulse chirping decreases the peak power and increases acquisition time, resulting in a much slower imaging speed compared to single-frame SRS using In this paper, we present deep learning algorithm solve inverse problem getting chemically labeled image from image. Our DenseNet-based method, termed as DeepChem, achieves...

Abstract Stimulated Raman scattering (SRS) microscopy allows for high-speed label-free chemical imaging of biomedical systems. The sensitivity SRS is limited to ~10 mM endogenous biomolecules. Electronic pre-resonant detection sub-micromolar chromophores. However, single biomolecules having extremely small cross-sections (~10 −30 cm 2 sr −1 ) remains unreachable. Here, we demonstrate plasmon-enhanced stimulated (PESRS) with single-molecule sensitivity. Incorporating pico-Joule laser...

Metabolic reprogramming in a subpopulation of cancer cells is hallmark tumor chemoresistance. However, single-cell metabolic profiling difficult because the lack method that can simultaneously detect multiple metabolites at level. In this study, through hyperspectral stimulated Raman scattering (hSRS) imaging carbon-hydrogen (C–H) window and sparsity-driven image decomposition, we demonstrate high-content hSRS (h 2 SRS) approach enables simultaneous mapping five major biomolecules, including...

Abstract Understanding metabolic heterogeneity is critical for optimizing microbial production of valuable chemicals, but requires tools that can quantify metabolites at the single‐cell level over time. Here, longitudinal hyperspectral stimulated Raman scattering (SRS) chemical imaging developed to directly visualize free fatty acids in engineered Escherichia coli many cell cycles. Compositional analysis also estimate chain length and unsaturation living cells. This method reveals...

Histological examination is crucial for cancer diagnosis, however, the labor-intensive sample preparation involved in histology impedes speed of diagnosis.Recently developed two-color stimulated Raman could bypass complex tissue processing to generates result close hematoxylin and eosin staining, which one golden standards histology.Yet, underlying chemical features are not revealed histology, compromising effectiveness prognostic stratification.Here, we present a high-content (HC-SRH)...

Abstract Photothermal microscopy is a highly sensitive pump-probe method for mapping nanostructures and molecules through the detection of local thermal gradients. While visible photothermal mid-infrared techniques have been developed, they possess inherent limitations. These either lack chemical specificity or encounter significant light attenuation caused by water absorption. Here, we present an overtone (OPT) technique that offers high specificity, sensitivity, spatial resolution...

Current nucleic acid-responsive DNA hydrogels face significant challenges, such as the requirement for high target concentrations, frequent redesigns, and increased costs, which limit their practical applications in biosensing. To address these issues, we developed a novel biosensing platform integrating CRISPR/Cas12a system into an RCA-based hydrogel. The hydrogel used could preencapsulate diverse signal molecules comprising GelRed, methylene blue, gold nanoparticles, were released upon...

Abstract High‐sensitivity chemical imaging offers a window to decipher the molecular orchestra inside living system. Based on vibrational fingerprint signatures, coherent Raman scattering microscopy provides label‐free approach map biomolecules and drug molecules cell. Yet, by near‐infrared (NIR) pulse excitation, sensitivity is limited millimolar concentration for endogenous biomolecules. Here, of stimulated (SRS) significantly boosted retinoid 34 micromolar via electronic preresonance in...

In this work, the effects of methacrylate monomers with various end groups (methyl, hydroxyl, epoxy, tetrahydrofuran, cyclohexane, benzene and siloxane) on morphologies, electro-optical mechanical properties polymer dispersed liquid crystal (PDLC) composite films were systematically investigated. The network morphologies samples prepared butyl methacrylate, tetrahydrofurfuryl cyclohexyl or benzyl observed, interestingly balls ball-networks formed by introducing hydroxypropyl glycidyl...

Abstract Enzyme‐instructed self‐assembly (EISA) is actively explored as a promising therapeutic approach for cancer treatment. However, the metabolic response of cells to EISA remains under‐studied. Here, by stimulated Raman scattering (SRS) imaging in C─H, fingerprint, and silent windows, it found that formation peptide assemblies within around significantly enhances both lipids catabolism fatty acids (FAs) uptake. It further increased uptake FAs aids resistance under treatment, likely cope...

As a stable and accurate biomarker, glycated hemoglobin (HbA1c) is clinically used to diagnose diabetes with threshold of 6.5% among total (Hb). Current methods such as boronate affinity chromatography involve complex processing large-volume blood samples. Moreover, these cannot measure HbA1c fraction at single-red cell (RBC) level, thus unable separate the contribution from other factors RBC lifetime. Here, we demonstrate spectroscopic transient absorption imaging approach that able...

Candida albicans (C. albicans), a major fungal pathogen, causes life-threatening infections in immunocompromised individuals. Fluconazole (FLC) is recommended as first-line therapy for treatment of invasive infections. However, the widespread use FLC has resulted increased antifungal resistance among different strains Candida, especially C. albicans, which leading source hospital-acquired Here, by hyperspectral stimulated Raman scattering imaging single cells fingerprint window and...