arXiv subjects

Hongjian He

Publications and source records attributed to Hongjian He.

12 recordsLinked to original sources

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

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 {\mu}M, 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↗

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

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

High-resolution myelin-water fraction and quantitative relaxation mapping using 3D ViSTa-MR fingerprinting

Purpose: This study aims to develop a high-resolution whole-brain multi-parametric quantitative MRI approach for simultaneous mapping of myelin-water fraction (MWF), T1, T2, and proton-density (PD), all within a clinically feasible scan time. Methods: We developed 3D ViSTa-MRF, which combined Visualization of Short Transverse relaxation time component (ViSTa) technique with MR Fingerprinting (MRF), to achieve high-fidelity whole-brain MWF and T1/T2/PD mapping on a clinical 3T scanner. To achieve fast acquisition and memory-efficient reconstruction, the ViSTa-MRF sequence leverages an optimized 3D tiny-golden-angle-shuffling spiral-projection acquisition and joint spatial-temporal subspace reconstruction with optimized preconditioning algorithm. With the proposed ViSTa-MRF approach, high-fidelity direct MWF mapping was achieved without a need for multi-compartment fitting that could introduce bias and/or noise from additional assumptions or priors. Results: The in-vivo results demonstrate the effectiveness of the proposed acquisition and reconstruction framework to provide fast multi-parametric mapping with high SNR and good quality. The in-vivo results of 1mm- and 0.66mm-iso datasets indicate that the MWF values measured by the proposed method are consistent with standard ViSTa results that are 30x slower with lower SNR. Furthermore, we applied the proposed method to enable 5-minute whole-brain 1mm-iso assessment of MWF and T1/T2/PD mappings for infant brain development and for post-mortem brain samples. Conclusions: In this work, we have developed a 3D ViSTa-MRF technique that enables the acquisition of whole-brain MWF, quantitative T1, T2, and PD maps at 1mm and 0.66mm isotropic resolution in 5 and 15 minutes, respectively. This advancement allows for quantitative investigations of myelination changes in the brain.

physics.med-ph↗

arXiv2022

Model-based Synthetic Data-driven Learning (MOST-DL): Application in Single-shot T2 Mapping with Severe Head Motion Using Overlapping-echo Acquisition

Use of synthetic data has provided a potential solution for addressing unavailable or insufficient training samples in deep learning-based magnetic resonance imaging (MRI). However, the challenge brought by domain gap between synthetic and real data is usually encountered, especially under complex experimental conditions. In this study, by combining Bloch simulation and general MRI models, we propose a framework for addressing the lack of training data in supervised learning scenarios, termed MOST-DL. A challenging application is demonstrated to verify the proposed framework and achieve motion-robust T2 mapping using single-shot overlapping-echo acquisition. We decompose the process into two main steps: (1) calibrationless parallel reconstruction for ultra-fast pulse sequence and (2) intra-shot motion correction for T2 mapping. To bridge the domain gap, realistic textures from a public database and various imperfection simulations were explored. The neural network was first trained with pure synthetic data and then evaluated with in vivo human brain. Both simulation and in vivo experiments show that the MOST-DL method significantly reduces ghosting and motion artifacts in T2 maps in the presence of unpredictable subject movement and has the potential to be applied to motion-prone patients in the clinic.

eess.IV↗

arXiv2021

Unified Style Transfer

Currently, it is hard to compare and evaluate different style transfer algorithms due to chaotic definitions of style and the absence of agreed objective validation methods in the study of style transfer. In this paper, a novel approach, the Unified Style Transfer (UST) model, is proposed. With the introduction of a generative model for internal style representation, UST can transfer images in two approaches, i.e., Domain-based and Image-based, simultaneously. At the same time, a new philosophy based on the human sense of art and style distributions for evaluating the transfer model is presented and demonstrated, called Statistical Style Analysis. It provides a new path to validate style transfer models' feasibility by validating the general consistency between internal style representation and art facts. Besides, the translation-invariance of AdaIN features is also discussed.

cs.CV↗

arXiv2021

Optimized multi-axis spiral projection MR fingerprinting with subspace reconstruction for rapid whole-brain high-isotropic-resolution quantitative imaging

Purpose: To improve image quality and accelerate the acquisition of 3D MRF. Methods: Building on the multi-axis spiral-projection MRF technique, a subspace reconstruction with locally low rank (LLR) constraint and a modified spiral-projection spatiotemporal encoding scheme termed tiny-golden-angle-shuffling (TGAS) were implemented for rapid whole-brain high-resolution quantitative mapping. The LLR regularization parameter and the number of subspace bases were tuned using retrospective in-vivo data and simulated examinations, respectively. B0 inhomogeneity correction using multi-frequency interpolation was incorporated into the subspace reconstruction to further improve the image quality by mitigating blurring caused by off-resonance effect. Results: The proposed MRF acquisition and reconstruction framework can produce provide high quality 1-mm isotropic whole-brain quantitative maps in a total acquisition time of 1 minute 55 seconds, with higher-quality results than ones obtained from the previous approach in 6 minutes. The comparison of quantitative results indicates that neither the subspace reconstruction nor the TGAS trajectory induce bias for T1 and T2 mapping. High quality whole-brain MRF data were also obtained at 0.66-mm isotropic resolution in 4 minutes using the proposed technique, where the increased resolution was shown to improve visualization of subtle brain structures. Conclusion: The proposed TGAS-SPI-MRF with optimized spiral-projection trajectory and subspace reconstruction can enable high-resolution quantitative mapping with faster acquisition speed.

physics.med-ph↗

arXiv2021

Reconstruction of Quantitative Susceptibility Maps from Phase of Susceptibility Weighted Imaging with Cross-Connected $Ψ$-Net

Quantitative Susceptibility Mapping (QSM) is a new phase-based technique for quantifying magnetic susceptibility. The existing QSM reconstruction methods generally require complicated pre-processing on high-quality phase data. In this work, we propose to explore a new value of the high-pass filtered phase data generated in susceptibility weighted imaging (SWI), and develop an end-to-end Cross-connected $Ψ$-Net (C$Ψ$-Net) to reconstruct QSM directly from these phase data in SWI without additional pre-processing. C$Ψ$-Net adds an intermediate branch in the classical U-Net to form a $Ψ$-like structure. The specially designed dilated interaction block is embedded in each level of this branch to enlarge the receptive fields for capturing more susceptibility information from a wider spatial range of phase images. Moreover, the crossed connections are utilized between branches to implement a multi-resolution feature fusion scheme, which helps C$Ψ$-Net capture rich contextual information for accurate reconstruction. The experimental results on a human dataset show that C$Ψ$-Net achieves superior performance in our task over other QSM reconstruction algorithms.

eess.IV↗

arXiv2020

Efficient T2 mapping with Blip-up/down EPI and gSlider-SMS (T2-BUDA-gSlider)

Purpose: To rapidly obtain high isotropic-resolution T2 maps with whole-brain coverage and high geometric fidelity. Methods: A T2 blip-up/down echo planar imaging (EPI) acquisition with generalized Slice-dithered enhanced resolution (T2-BUDA-gSlider) is proposed. A radiofrequency (RF)-encoded multi-slab spin-echo EPI acquisition with multiple echo times (TEs) was developed to obtain high SNR efficiency with reduced repetition time (TR). This was combined with an interleaved 2-shot EPI acquisition using blip-up/down phase encoding. An estimated field map was incorporated into the joint multi-shot EPI reconstruction with a structured low rank constraint to achieve distortion-free and robust reconstruction for each slab without navigation. A Bloch simulated subspace model was integrated into gSlider reconstruction and utilized for T2 quantification. Results: In vivo results demonstrated that the T2 values estimated by the proposed method were consistent with gold standard spin-echo acquisition. Compared to the reference 3D fast spin echo (FSE) images, distortion caused by off-resonance and eddy current effects were effectively mitigated. Conclusion: BUDA-gSlider SE-EPI acquisition and gSlider-subspace joint reconstruction enabled distortion-free whole-brain T2 mapping in 2 min at ~1 mm3 isotropic resolution, which could bring significant benefits to related clinical and neuroscience applications.

physics.med-ph↗

arXiv2019

Robust diffusion parametric mapping of motion-corrupted data with a three-dimensional convolutional neural network

Head motion is inevitable in the acquisition of diffusion-weighted images, especially for certain motion-prone subjects and for data gathering of advanced diffusion models with prolonged scan times. Deficient accuracy of motion correction cause deterioration in the quality of diffusion model reconstruction, thus affecting the derived measures. This results in either loss of data, or introducing bias in outcomes from data of different motion levels, or both. Hence minimizing motion effects and reutilizing motion-contaminated data becomes vital to quantitative studies. We have previously developed a 3-dimensional hierarchical convolution neural network (3D H-CNN) for robust diffusion kurtosis mapping from under-sampled data. In this study, we propose to extend this method to motion-contaminated data for robust recovery of diffusion model-derived measures with a process of motion assessment and corrupted volume rejection. We validate the proposed pipeline in two in-vivo datasets. Results from the first dataset of individual subjects show that all the diffusion tensor and kurtosis tensor-derived measures from the new pipeline are minimally sensitive to motion effects, and are comparable to the motion-free reference with as few as eight volumes retained from the motion-contaminated data. Results from the second dataset of a group of children with attention deficit hyperactivity disorder demonstrate the ability of our approach in ameliorating spurious group differences due to head motion. This method shows great potential for exploiting some valuable but motion-corrupted DWI data which are likely to be discarded otherwise, and applying to data with different motion level thus improving their utilization and statistic power.

physics.med-ph↗

arXiv2019

Ultrashort Echo Time Magnetic Resonance Fingerprinting (UTE-MRF) for Simultaneous Quantification of Long and Ultrashort T2 Tissues

Purpose: To demonstrate an ultrashort echo time magnetic resonance fingerprinting (UTE-MRF) method that can simultaneously quantify tissue relaxometries for muscle and bone in musculoskeletal systems and tissue components in brain and therefore can synthesize pseudo-CT images. Methods: A FISP-MRF sequence with half pulse excitation and half spoke radial acquisition was designed to sample fast T2 decay signals. Sinusoidal echo time (TE) pattern was applied to enhance MRF sensitivity for tissues with short and ultrashort T2 values. The performance of UTE-MRF was evaluated via simulations, phantoms, and in vivo experiments. Results: A minimal TE of 0.05 ms was achieved in UTE-MRF. Simulations indicated that extension of TE sampling increased T2 quantification accuracy in cortical bone and tendon, and had little impact on long T2 muscle quantifications. For a rubber phantom, an average T1/T2 of 162/1.07 ms from UTE-MRF were compared well with gold standard T2 of 190 ms from IR-UTE and T2* of 1.03 ms from UTE sequence. For a long T2 agarose phantom, the linear regression slope between UTE-MRF and gold standard was 1.07 (R2=0.991) for T1 and 1.04 (R2=0.994) for T2. In vivo experiments showed the detection of cortical bone and Achilles tendon, where the averaged T2 was respectively 1.0 ms and 15 ms. Scalp images were in good agreement with CT. Conclusion: UTE-MRF with sinusoidal TE variations shows its capability to produce pseudo-CT images and simultaneously output T1, T2, proton density, and B0 maps for tissues with long T2 and short/ultrashort T2 in the brain and musculoskeletal system.

physics.med-ph↗