arXiv subjects

Ji-Xin Cheng

Publications and source records attributed to Ji-Xin Cheng.

At least 19 recordsLinked to original sources

arXiv2026

FILM: Mapping organellar metabolism by mid-infrared photothermal modulated fluorescence

Metabolism unfolds within specific organelles in eukaryotic cells. Lysosomes are highly metabolically active organelles, and their metabolic states dynamically influence signal transduction, cellular homeostasis, and organismal physiopathology. Despite the significance of lysosomal metabolism, a method for its in vivo measurement is currently lacking. Here, we report optical boxcar-enhanced, fluorescence-detected mid-infrared photothermal microscopy, together with AI-assisted data denoising and spectral deconvolution, to map metabolic activity and composition of individual lysosomes in living cells and organisms. Using this method, we uncovered lipolysis and proteolysis heterogeneity across lysosomes within the same cell, as well as early-onset lysosomal dysfunction during organismal aging. Additionally, we discovered organelle-level metabolic changes associated with diverse lysosomal storage diseases. This method holds the broad potential to profile metabolic fingerprints of individual organelles within their native context and quantitatively assess their dynamic changes under different physiological and pathological conditions, providing a high-resolution chemical cellular atlas.

physics.bio-ph↗

arXiv2026

Sub-micromolar imaging of intrinsic chromophores by two-photon photothermal microscopy captures mitochondrial response to chemotherapy

Intracellular chromophores (e.g., NADH and FAD) play a central role in regulation of cellular metabolism. Though autofluorescence has been extensively used for label-free mapping of chromophores inside a cell, its sensitivity and molecular specificity are constrained by the low quantum yield and the fluorescence spectral overlap. Here, we address these challenges by employing a photothermal approach to measure the optical absorption of chromophores rather than its autofluorescence. By combining near-infrared pump and visible probe beams, our two-photon photothermal (2PPT) microscope exploits localized thermal transients generated through two-photon absorption, enabling detection of chromophore-specific signatures beyond the reach of autofluorescence. We demonstrate sub-micromolar limit of detection for the metabolic coenzymes NADH and FAD of 0.87 uM and 0.99 uM, respectively. Such high sensitivity enables differentiating the influence of different mitochondria shapes on metabolism activity. Importantly, the fluorescence crosstalk-free 2PPT can identify the biomolecular source of contrast from cellular mitochondria in a label-free manner based on spectroscopy. 2PPT microscopy is utilized to study metabolic alterations of mitochondria in cancer under chemotherapy at the single organelle level.

physics.optics↗

arXiv2026

Label-free Imaging of Single-Biomolecule Structure and Interaction by Stimulated Raman Photothermal Encoded Scattering

Current single molecule methods either rely on fluorescence or lack chemical information. Here we report stimulated Raman photothermal encoded scattering (SRPSCAT) microscopy for quantitative bond-selective imaging of single-biomolecule structures and interactions in native environments. In this approach, scattering of the target molecule is modulated by the deposited energy from stimulated Raman gain and loss processes, thereby encoding vibrational spectroscopic information. Leveraging single-molecule sensitivity of interferometric scattering, SRPSCAT can map single proteins with chemical specificity, determine their mass, and distinguish protein secondary structures based on their Raman fingerprints. Furthermore, single protein binding kinetics are quantified and the conformational dynamics of single de novo designed allosteric proteins are observed. Together, these results highlight the potential of SRPSCAT for label-free structural, functional and dynamic analysis at the single-molecule level.

physics.bio-ph↗

arXiv2026

Mid-wave infrared photothermal microscopy for molecular and metabolic imaging in deep tissues and spheroids

High-resolution chemical imaging within deep tissues and intact spheroids remains a grand challenge. Here, we introduce mid-wave infrared photothermal (MWIP) microscopy operating in the underexplored 2000-2500 nm spectral window for submicron-resolution molecular and metabolic imaging in intact tumor spheroids and deep tissues. A dark-field photothermal detection scheme significantly suppresses water background and enhances contrast. By accessing strong carbon-hydrogen combination absorptions, a detection limit of 0.12% for dimethyl sulfoxide is achieved, comparable to stimulated Raman scattering microscopy. Depth-resolved imaging of endogenous biomolecules up to 500 micrometers in excised mouse skin and brain tissues is demonstrated. MWIP further enables depth-resolved tracking of transdermal drug transport via carbon-deuterium overtone absorption. Using deuterium metabolic probes, fatty-acid metabolism is imaged at 200 micrometers deep within intact tumor spheroids through carbon-deuterium overtone and combination bands. Collectively, MWIP offers a platform for functional imaging of 3D biological systems in their native environments.

physics.optics↗

arXiv2026

Transfer-Function Approach to Substrate-Enhanced Diffraction Tomography

Forward and backward scattering provide complementary volumetric and interfacial information, yet conventional three-dimensional (3D) imaging typically accesses only one. In this Letter, we present a substrate-enhanced diffraction tomography approach that simultaneously recovers both channels under multi-angle epi-illumination.This geometry captures one forward- and two backward-scattering bands in axially symmetric Fourier regions, where their complementary coverage enables phase-absorption separation in a non-Hermitian spectrum. Explicit 3D transfer functions are derived for both channels, and an axial Kramers-Kronig relation is established to incorporate substrate-induced boundary conditions in a unified framework. Our results establish a label-free, high-resolution 3D imaging modality that surpasses the limits of existing methods.

physics.optics↗

arXiv2026

Single-pulse Stimulated Raman Photothermal Microscopy and Direct Visualization of Cholesterol-rich Membrane Domains

By measuring the thermal effects resulting from stimulated Raman excitations, stimulated Raman photothermal (SRP) microscope offers a new access to spatially and temporally resolved Raman signatures across various sample types. Unlike stimulated Raman scattering (SRS) microscopy, SRP is highly compatible with noisy ultrafast laser sources, allowing the use of high peak power, low repetition rate optical parametric amplifier (OPA) lasers to boost sensitivity and imaging speed. Here, we report a single pulse SRP (spSRP) microscope system in which SRP signals are induced by individual pairs of laser pulses generated by an OPA laser. Extensive pulse chirping is used to maximize SRS excitation rate and to minimize photodamage. The single-pixel limit of detection (LOD) of spSRP on dimethyl sulfoxide (DMSO) reaches 890 μM, which is a ~44-fold improvement over SRS microscope. Versatile applications to fungi, cells, and tissues are demonstrated. Live cell spSRP imaging was carried out at speed of 10 frames per second. Particularly, the spSRP system enables direct visualization of cholesterol-rich domains, co-localized with caveolin immunofluorescence, in the plasma membrane of HeLa cells.

physics.optics↗

arXiv2026

Chem-SIM: Super-resolution Chemical Imaging via Photothermal Modulation of Structured-Illumination Fluorescence

Structured illumination microscopy (SIM) has attained high spatiotemporal delineation of subcellular architecture, yet offers limited insight into chemical composition. We develop Chem-SIM, a structured-illumination fluorescence detected mid-infrared photothermal microscopy, for super-resolved chemical imaging of microorganisms and mammalian cells. Poisson maximum-likelihood demodulation and spectral normalization across wavenumber recover the weak IR-induced fluorescence intensity change under low photon budgets and convert the fluorescence intensity modulation to chemical fingerprints. Photothermal gating further rejects water backgrounds in aqueous samples, while the IR pump maintains cellular activity at near-physiological temperature. Chem-SIM preserves full vibrational fingerprints, achieves SIM-grade lateral resolution in a high-throughput camera-based format. Here, we show that this platform distinguishes stationary- from log-phase bacteria through chemical content mapping, reports deuterated fatty-acid incorporation in ovarian cancer cells, and resolves lipid-droplet dynamics in live cells, establishing a high-throughput route to super-resolved imaging of organelle chemistry, metabolism, and dynamics.

physics.optics↗

arXiv2026

Micromolar chemical imaging by high-energy low-photodamage Coherent Anti-stokes Raman Scattering (HELP-CARS)

Coherent anti-Stokes Raman scattering (CARS) microscopy offers label-free chemical imaging capabilities, but its performance is constrained by small Raman scattering cross-section, strong non-resonant background (NRB), and limited signal-to-noise ratio (SNR). Here, we introduce a high-energy, low-photodamage CARS (HELP-CARS) platform designed to overcome these physical limitations. By employing a 1-MHz non-collinear optical parametric amplifier (NOPA) with extensive pulse chirping, HELP-CARS increases the coherent Raman excitation efficiency by ~300 times and improves the signal-to-nonresonant background ratio by 11 times, while inducing negligible damage during live cell imaging. Furthermore, to remove non-independent noise and physically entangled non-resonant background, we incorporate self-supervised deep-learning denoising and background removal based on the Kramers-Kronig relationship, yielding sensitivity improvement by an additional order of magnitude. Together, these advances provide a micromolar imaging sensitivity (160 uM for Dimethyl sulfoxide-d6) corresponding to 1000 molecules in the focal volume. Such high sensitivity enables high-fidelity chemical imaging in both fingerprint and silent windows. Hyperspectral HELP-CARS imaging of deuterated fatty acids allowed first observation of chemical separation with single lipid droplet. Together, HELP-CARS offers a powerful and generalizable approach for ultrasensitive and quantitative vibrational imaging of biological systems.

physics.optics↗

arXiv2025

Mid-Infrared Photothermal Relaxation Intensity Diffraction Tomography for Video-rate Volumetric Chemical Imaging

Three-dimensional molecular imaging of living cells is essential for unraveling cellular metabolism and response to therapies. However, existing volumetric methods, including fluorescence microscopy and quantitative phase imaging, either require fluorescent labels or lack chemical specificity. Mid-infrared (mid-IR) photothermal microscopy provides label-free spectroscopic contrast with sub-micrometer resolution but is limited by slow acquisition rates, precluding 3D live-cell studies. Here, we present a photothermal relaxation intensity diffraction tomography (PRIDT) system that encodes mid-IR absorption induced refractive index change via a photothermal relaxation scheme and recovers it through intensity diffraction tomography. PRIDT achieves video-rate volumetric chemical imaging with up to 15 Hz per wavelength and offers lateral and axial resolutions of 264 nm and 1.12 um over a volumetric field of view of 50x50x10 um3. We showcase high-speed PRIDT imaging of protein and lipid metabolism in ovarian cancer cells and lipid-droplet dynamics in live cells. PRIDT opens new avenues for rapid, quantitative, three-dimensional molecular imaging in living systems.

physics.optics↗

arXiv2025

Miniaturized optically-generated Bessel beam ultrasound for volumetric transcranial brain stimulation

Non-invasive stimulation of small, variably shaped brain sub-regions is crucial for advancing our understanding of brain functions. Current ultrasound neuromodulation faces two significant trade-offs when targeting brain sub-regions: miniaturization versus volumetric control and spatial resolution versus transcranial capability. Here, we present an optically-generated Bessel beam ultrasound (OBUS) device designed to overcome these limitations. This 2.33 mm-diameter miniaturized device delivers a column-shaped field achieving a lateral resolution of 152 um and an axial resolution of 1.93 mm, targeting brain sub-regions with an elongated volume of tissue activation. Immunofluorescence imaging of mouse brain slices confirms its ability to stimulate cells at a depth of 2.2 mm. Additionally, OBUS outperforms conventional Gaussian ultrasound in transcranial transmission efficiency and beam shape preservation. Electrophysiological recordings and functional MRI captured rodent brain responses evoked by OBUS, demonstrating OBUS's ability to non-invasively activate neural circuits in intact brains. This technology offers new possibilities for studying brain functions with precision and volumetric control.

q-bio.NC↗

arXiv2025

Fiber laser based stimulated Raman photothermal microscopy with long working distance optics

Stimulated Raman scattering (SRS) microscopy is a highly sensitive chemical imaging technique. However, the broader application of SRS has been limited by two key challenges: the reliance on low-noise but bulky solid-state laser sources and stringent sample requirements necessitated by high numerical aperture (NA) optics. Here, we present a fiber laser based stimulated Raman photothermal (SRP) microscope that addresses these limitations. While appreciating the portability and compactness of a noisy source, fiber laser SRP enables a two-order-of-magnitude improvement in signal to noise ratio over fiber laser SRS without balance detection. Furthermore, with the use of low NA, long working distance optics for signal collection, SRP expands the allowed sample space from millimeters to centimeters, which diversifies the sample formats to multi-well plates and thick tissues. The sensitivity and imaging depth are further amplified by using urea for both thermal enhancement and tissue clearance. Together, fiber laser SRP microscopy provides a robust, user-friendly platform for diverse applications.

physics.optics↗

arXiv2025

Spatial-offset pump-probe imaging of nonradiative dynamics at optical resolution

Nonradiative photothermal (PT) and photoacoustic (PA) processes have found widespread applications in imaging, stimulation, and therapy. Mapping the generation and propagation of PA and PT waves with resolution is important to elucidate how these fields interact with biological systems. To this end, we introduce spatial offset pump-probe imaging (SOPPI). By spatially offsetting the pump beam and the probe beam, SOPPI can image simultaneously PA and PT wave propagation with nanosecond temporal resolution, micrometer spatial resolution, 65 MHz detection bandwidth, and a sensitivity of 9.9 Pa noise equivalent pressure. We first map the PA and PT evolution from a fiber emitter, and how the wave interacting with a mouse skull and brain slices. SOPPI imaging of PA waves from a tapered fiber with water as an absorber shows a wavelength-dependent generation, evanescent wave generated PA, and back-propagated acoustic Mach Cone. At last, a SOPPI-PACT is developed to reconstruct the pigment distribution inside a zebrafish larva with high precision and signal-to-noise ratio.

physics.optics↗

arXiv2024

Mid-infrared Energy Deposition Spectroscopy

Photothermal microscopy is an emerging tool for measuring light-matter interactions with single-molecule sensitivity. It is generally believed that the spectral acquisition speed in photothermal microscopy is limited by the slow thermal diffusion process. Here, we demonstrate mid-infrared energy deposition (MIRED) spectroscopy, which offers both microsecond-scale temporal resolution and sub-micron spatial resolution. In this approach, the photothermal process is optically probed while the infrared pulses from a quantum cascade laser array are rapidly tuned. Based on Newton's law, the energy deposition corresponds to the first derivative of local temperature rise over time and provides the instantaneous infrared absorption. By employing time-resolved measurement of transient energy deposition, the upper limit for spectrum encoding shifts to the vibrational relaxation level, which occurs on the picosecond scale. This method significantly increases the detection bandwidth while maintaining the sensitivity and resolution advantages of photothermal detection.

physics.optics↗

arXiv2024

Self-Supervised Elimination of Non-Independent Noise in Hyperspectral Imaging

Hyperspectral imaging has been widely used for spectral and spatial identification of target molecules, yet often contaminated by sophisticated noise. Current denoising methods generally rely on independent and identically distributed noise statistics, showing corrupted performance for non-independent noise removal. Here, we demonstrate Self-supervised PErmutation Noise2noise Denoising (SPEND), a deep learning denoising architecture tailor-made for removing non-independent noise from a single hyperspectral image stack. We utilize hyperspectral stimulated Raman scattering and mid-infrared photothermal microscopy as the testbeds, where the noise is spatially correlated and spectrally varied. Based on single hyperspectral images, SPEND permutates odd and even spectral frames to generate two stacks with identical noise properties, and uses the pairs for efficient self-supervised noise-to-noise training. SPEND achieved an 8-fold signal-to-noise improvement without having access to the ground truth data. SPEND enabled accurate mapping of low concentration biomolecules in both fingerprint and silent regions, demonstrating its robustness in sophisticated cellular environments.

eess.IV↗

arXiv2023

Millimeter-deep micron-resolution vibrational imaging by shortwave infrared photothermal microscopy

Deep-tissue chemical imaging plays a vital role in biological and medical applications. Here, we present a shortwave infrared photothermal (SWIP) microscope for millimeter-deep vibrational imaging with sub-micron lateral resolution and nanoparticle detection sensitivity. By pumping the overtone transition of carbon-hydrogen bonds and probing the subsequent photothermal lens with shortwave infrared light, SWIP can obtain chemical contrast from microparticles located millimeter-deep in a highly scattering phantom. By fast digitization on the optically probed signal, the amplitude of photothermal signal is shown to be 63 times larger than that of photoacoustic signal, thus enabling highly sensitive detection of nanoscale objects. SWIP can resolve the intracellular lipids across an intact tumor spheroid and the layered structure in millimeter-thick liver, skin, brain, and breast tissues. Together, SWIP microscopy fills a gap in vibrational imaging with sub-cellular resolution and millimeter-level penetration, which heralds broad potential for life science and clinical applications.

physics.optics↗

arXiv2023

High-content stimulated Raman histology of human breast cancer

Histological examination is crucial for cancer diagnosis, including hematoxylin and eosin (H&E) staining for mapping morphology and immunohistochemistry (IHC) staining for revealing chemical information. Recently developed two-color stimulated Raman histology could bypass the complex tissue processing to mimic H&E-like morphology. Yet, the underlying chemical features are not revealed, compromising the effectiveness of prognostic stratification. Here, we present a high-content stimulated Raman histology (HC-SRH) platform that provides both morphological and chemical information for cancer diagnosis based on un-stained breast tissues. Through spectral unmixing in the C-H vibration window, HC-SRH can map unsaturated lipids, cellular protein, extracellular matrix, saturated lipid, and water in breast tissue. In this way, HC-SRH provides excellent contrast for various tissue components. Considering rapidness is important in clinical trials, we implemented spectral selective sampling to boost the speed of HC-SRH by one order. We also successfully demonstrated the HC-SRH in a clinical-compatible fiber laser-based SRS microscopy. With the widely rapid tuning capability of the advanced fiber laser, a clear chemical contrast of nucleic acid and solid-state ester is shown in the fingerprint result.

q-bio.TO↗

arXiv2023

Single virus fingerprinting by widefield interferometric defocus-enhanced mid-infrared photothermal microscopy

Clinical identification and fundamental study of viruses rely on the detection of viral proteins or viral nucleic acids. Yet, amplification-based and antigen-based methods are not able to provide precise compositional information of individual virions due to small particle size and low-abundance chemical contents (e.g., ~ 5000 proteins in a vesicular stomatitis virus). Here, we report a widefield interferometric defocus-enhanced mid-infrared photothermal (WIDE-MIP) microscope for high-throughput fingerprinting of single viruses. With the identification of feature absorption peaks, WIDE-MIP reveals the contents of viral proteins and nucleic acids in single DNA vaccinia viruses and RNA vesicular stomatitis viruses. Different nucleic acids signatures of thymine and uracil residue vibrations are obtained to differentiate DNA and RNA viruses. WIDE-MIP imaging further reveals an enriched \b{eta} sheet components in DNA varicella-zoster virus proteins. Together, these advances open a new avenue for compositional analysis of viral vectors and elucidating protein function in an assembled virion.

physics.optics↗

arXiv2023

Far-field Super-resolution Chemical Microscopy

Far-field chemical microscopy providing molecular electronic or vibrational fingerprint information opens a new window for the study of three-dimensional biological, material, and chemical systems. Chemical microscopy provides a nondestructive way of chemical identification without exterior labels. However, the diffraction limit of optics hindered it from discovering more details under the resolution limit. Recent development of super-resolution techniques gives enlightenment to open this door behind far-field chemical microscopy. Here, we review recent advances that have pushed the boundary of far-field chemical microscopy in terms of spatial resolution. We further highlight applications in biomedical research, material characterization, environmental study, cultural heritage conservation, and integrated chip inspection.

physics.optics↗