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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Deep Learning on Multimodal Chemical and Whole Slide Imaging Data for Predicting Prostate Cancer Directly from Tissue Images

Prostate cancer is one of the most common cancers globally and is the second most common cancer in the male population in the US. Here we develop a study based on correlating the hematoxylin and eosin (H&E)-stained biopsy data with MALDI mass-spectrometric imaging data of the corresponding tissue to determine the cancerous regions and their unique chemical signatures and variations of the predicted regions with original pathological annotations. We obtain features from high-resolution optical micrographs of whole slide H&E stained data through deep learning and spatially register them with mass spectrometry imaging (MSI) data to correlate the chemical signature with the tissue anatomy of the data. We then use the learned correlation to predict prostate cancer from observed H&E images using trained coregistered MSI data. This multimodal approach can predict cancerous regions with ~80% accuracy, which indicates a correlation between optical H&E features and chemical information found in MSI. Further, we show that such paired multimodal data can be used for training feature extraction networks on H&E data which bypasses the need to acquire expensive MSI data and eliminates the need for manual annotation saving valuable time. Two chemical biomarkers were also found to be predicting the ground truth cancerous regions. This study shows promise in generating improved patient treatment trajectories by predicting prostate cancer directly from readily available H&E-stained biopsy images aided by coregistered MSI data.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Ambient Single-Cell Analysis and Native Tissue Imaging Using Laser-Ablation Electrospray Ionization Mass Spectrometry with Increased Spatial Resolution

Laser ablation electrospray ionization mass spectrometry (LAESI-MS) is an emerging method that has the potential to transform the field of metabolomics. This is in part due to LAESI-MS being an ambient ionization method that requires minimal sample preparation and uses (endogenous) water for in situ analysis. This application note details the employment of the ‘LAESI microscope’ source to perform spatially resolved MS analysis of cells and MS imaging (MSI) of tissues at high spatial resolution. This source configuration utilizes a long-working distance reflective objective that permits both visualization of the sample and a smaller LAESI laser beam profile than conventional LAESI setups. In this work, we analyzed 200 single cells of Allium cepa (red onion) and imaged Fittonia argyroneura (nerve plant) in high spatial resolution using this source coupled to a Fourier transform mass spectrometer for high mass resolution and high mass accuracy metabolomics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Superconducting nanowire single-photon detector enhanced near-infrared II portable confocal microscopy for tissue imaging with indocyanine green

In this Letter a novel, to our knowledge, approach for near-infrared (NIR) fluorescence portable confocal microscopy is introduced, aiming to enhance fluorescence imaging of biological samples in the NIR-II window. By integrating a superconducting nanowire single-photon detector (SNSPD) into a confocal microscopy, we have significantly leveraged the detection efficiency of the NIR-II fluorescence signal from indocyanine green (ICG), an FDA-approved dye known for its NIR-II fluorescence capabilities. The SNSPD, characterized by its extremely low dark count rate and optimized NIR system detection efficiency, enables the excitation of ICG with 1 mW and the capture of low-light fluorescence signals from deep regions (up to 512 µm). Consequently, our technique was able to produce high-resolution images of bio samples with a superior signal-to-noise ratio, making a substantial advancement in the field of fluorescence microscopy and offering a promising opportunity for future clinical study.

Liu, Yifan (ORCID:0000000328877704)↗
DOE OSTI2026

Three-dimensional high-content imaging of unstained soft tissue with subcellular resolution using a laboratory-based X-ray microscope

With increasing interest in studying biological systems across spatial scales—from centimeters down to nanometers—histology continues to be the gold standard for tissue imaging at cellular resolution, providing an essential bridge between macroscopic and nanoscopic analysis. However, its inherently destructive and two-dimensional nature limits its ability to capture the full three-dimensional complexity of tissue architecture. Here, we show that phase-contrast X-ray microscopy can enable three-dimensional virtual histology with subcellular resolution. This technique provides direct quantification of electron density without restrictive assumptions, allowing for direct characterization of cellular nuclei in a standard laboratory setting. By combining high spatial resolution and soft tissue contrast, with automated segmentation of cell nuclei, we demonstrated virtual Hematoxylin and Eosin (H&E) staining using machine learning-based style transfer, yielding volumetric datasets compatible with existing histopathological analysis tools. Furthermore, by integrating electron density and the sensitivity to nanometric features of the dark field contrast channel, we achieve stain-free, high-content imaging capable of distinguishing nuclei and extracellular matrix.

3D virtual histology↗
DOE OSTI2024

Adaptive optical third-harmonic generation microscopy for in vivo imaging of tissues

Third-harmonic generation microscopy is a powerful label-free nonlinear imaging technique, providing essential information about structural characteristics of cells and tissues without requiring external labelling agents. In this work, we integrated a recently developed compact adaptive optics module into a third-harmonic generation microscope, to measure and correct for optical aberrations in complex tissues. Taking advantage of the high sensitivity of the third-harmonic generation process to material interfaces and thin membranes, along with the 1,300-nm excitation wavelength used here, our adaptive optical third-harmonic generation microscope enabled high-resolution in vivo imaging within highly scattering biological model systems. Examples include imaging of myelinated axons and vascular structures within the mouse spinal cord and deep cortical layers of the mouse brain, along with imaging of key anatomical features in the roots of the model plant Brachypodium distachyon. In all instances, aberration correction led to enhancements in image quality.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

NaroNet: Discovery of tumor microenvironment elements from highly multiplexed images

Understanding the spatial interactions between the elements of the tumor microenvironment -i.e. tumor cells. fibroblasts, immune cells- and how these interactions relate to the diagnosis or prognosis of a tumor is one of the goals of computational pathology. We present NaroNet, a deep learning framework that models the multi-scale tumor microenvironment from multiplex-stained cancer tissue images and provides patient-level interpretable predictions using a seamless end-to-end learning pipeline. Trained only with multiplex-stained tissue images and their corresponding patient-level clinical labels, NaroNet unsupervisedly learns which cell phenotypes, cell neighborhoods, and neighborhood interactions have the highest influence to predict the correct label. To this end, NaroNet incorporates several novel and state-of-the-art deep learning techniques, such as patch-level contrastive learning, multi-level graph embeddings, a novel max-sum pooling operation, or a metric that quantifies the relevance that each microenvironment element has in the individual predictions. We validate NaroNet using synthetic data simulating multiplex-immunostained images where a patient label is artificially associated to the -adjustable- probabilistic incidence of different microenvironment elements. We then apply our model to two sets of images of human cancer tissues: 336 seven-color multiplex-immunostained images from 12 high-grade endometrial cancer patients; and 382 35-plex mass cytometry images from 215 breast cancer patients. In both synthetic and real datasets, NaroNet provides outstanding predictions of relevant clinical information while associating those predictions to the presence of specific microenvironment elements.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Computational microscopy for fast widefield deep-tissue fluorescence imaging using a commercial dual-cannula probe

A solid-glass cannula serves as a micro-endoscope that can deliver excitation light deep inside tissue while also collecting emitted fluorescence. Then, we utilize deep neural networks to reconstruct images from the collected intensity distributions. By using a commercially available dual-cannula probe, and training a separate deep neural network for each cannula, we effectively double the field of view compared to prior work. We demonstrated ex vivo imaging of fluorescent beads and brain slices and in vivo imaging from whole brains. We clearly resolved 4 µm beads, with FOV from each cannula of 0.2 mm (diameter), and produced images from a depth of ∼1.2 mm in the whole brain, currently limited primarily by the labeling. Since no scanning is required, fast widefield fluorescence imaging limited primarily by the brightness of the fluorophores, collection efficiency of our system, and the frame rate of the camera becomes possible.

42 ENGINEERING↗
DOE OSTI2025

Coherent optical imaging of moving objects hidden in a heavily scattering random medium

Experimental results are presented that provide insight into the physics of statistical imaging in heavily scattering random media based on measured speckle correlations as a function of the change in position of a moving object. In this way, definitive interpretation of a rather complex and earlier theory is achieved, making this work an experimental complement to that theory paper []. Motion could be natural, where the set of positions is estimated or separately obtained, or directed, where a mechanical stage can be used to adjust the object's position. In the experiment, a coherent laser illuminates two scattering diffusers, while an object is translated between them in the resulting speckled field and images are collected in a transmission configuration. Results are shown for various objects of differing size and geometry, allowing the theory to be validated and interpreted with new understanding. This work demonstrates imaging opportunities, and applications include material characterization, environmental imaging and sensing, and deep-tissue imaging. Published by the American Physical Society 2025

Hastings, Ryan L. (ORCID:0009000095977807)↗
DOE OSTI2022

Fully Integrated Ultra-thin Intraoperative Micro-imager for Cancer Detection Using Upconverting Nanoparticles

Abstract Purpose Intraoperative detection and removal of microscopic residual disease (MRD) remain critical to the outcome of cancer surgeries. Today’s minimally invasive surgical procedures require miniaturization and surgical integration of highly sensitive imagers to seamlessly integrate into the modern clinical workflow. However, current intraoperative imagers remain cumbersome and still heavily dependent on large lenses and rigid filters, precluding further miniaturization and integration into surgical tools. Procedures We have successfully engineered a chip-scale intraoperative micro-imager array—without optical filters or lenses—integrated with lanthanide-based alloyed upconverting nanoparticles (aUCNPs) to achieve tissue imaging using a single micro-chip. This imaging platform is able to leverage the unique optical properties of aUCNPs (long luminescent lifetime, high-efficiency upconversion, no photobleaching) by utilizing a time-resolved imaging method to acquire images using a 36-by-80-pixel, 2.3 mm $$\times$$ × 4.8 mm silicon-based electronic imager micro-chip, that is, less than 100-µm thin. Each pixel incorporates a novel architecture enabling automated background measurement and cancellation. We have validated the performance, spatial resolution, and the background cancellation scheme of the imaging platform, using resolution test targets and mouse prostate tumor sample intratumorally injected with aUCNPs. To demonstrate the ability to image MRD, or tumor margins, we evaluated the imaging platform in visualizing a single-cell thin section of the injected prostate tumor sample. Results Tested on USAF resolution targets, the imager is able to achieve a resolution of 71 µm. We have also demonstrated successful background cancellation, achieving a signal-to-background ratio of 8 when performing ex vivo imaging on aUCNP-injected prostate tumor sample, improved from originally 0.4. The performance of the imaging platform on single-cell layer sections was also evaluated and the sensor achieved a signal-to-background ratio of 4.3 in resolving cell clusters with sizes as low as 200 cells. Conclusion The imaging system proposed here is a scalable chip-scale ultra-thin alternative for bulky conventional intraoperative imagers. Its novel pixel architecture and background correction scheme enable visualization of microscopic-scale residual disease while remaining completely free of lenses and filters, achieving an ultra-miniaturized form factor—critical for intraoperative settings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Three Photon Excited Image Scanning Microscopy for in-Depth Super-Resolution Studies of Biological Samples

Multiphoton laser scanning microscopy is a powerful tool for deep imaging of thick biological samples. Image scanning microscopy (ISM) has demonstrated significant improvements in the signal-to-noise ratio in confocal laser scanning microscopy, while at the same time improving upon the effectively attainable resolution. Two-photon excitation (2PE), combined with ISM, has been shown to allow for deep tissue imaging with enhanced resolution compared to 2PE microscopy. Three-photon excitation (3PE) has enabled record imaging depth and contrast for multiphoton imaging, due to the superior suppression of out-of-focus signal generation. In this paper, we demonstrate super-resolution 3PE ISM. This is achieved using a single-photon avalanche detector array, and 1040-nm pulses for 3PE of blue fluorescence. This method enables subdiffraction limited resolution imaging of biological samples stained with blue fluorescent markers, such as mouse myocardial and spinal cord tissues stained with 4 ′ , 6 -diamidino-2-phenylindole. Deconvolution improves the resolving power further and allows for imaging with better than λ / 8 resolution with respect to the 3PE wavelength λ . With the ISM pixel reassignment procedure, we demonstrate a resolution enhancement of ∼ 1.6 laterally, compared to the resolution attained using a photomultiplier tube in a non-descanned detection arrangement, and a factor of ∼ 1.8 enhancement in axial resolution. The experimentally measured three-dimensional point spread function volume is shrunk ∼ 4.4 -fold, which is close to the theoretically expected enhancement. Published by the American Physical Society 2024

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Direct Observation of Circularly Polarized Nonlinear Optical Activities in Chiral Hybrid Lead Halides

Circularly polarized light emission is a crucial application in imaging, sensing, and photonics. However, utilizing low-energy photons to excite materials, as opposed to high-energy light excitation, can facilitate deep-tissue imaging and sensing applications. The challenge lies in finding materials capable of directly generating circularly polarized nonlinear optical effects. In this study, we introduce a chiral hybrid lead halide (CHLH) material system, R/S-DPEDPb 3 Br 8 ·H 2 O (DPED = 1,2-diphenylethylenediammonium), which can directly produce circularly polarized second harmonic generation (CP-SHG) through linearly polarized infrared light excitation, exhibiting a polarization efficiency as high as 37% at room temperature. To understand the spin relaxation mechanisms behind the high polarization efficiency, we utilized two models, so-called D’yakonov–Perel’ (DP) and Bir–Aronov–Pikus (BAP) mechanisms. The unique zigzag inorganic frameworks within the hybrid structure are believed to reduce the dielectric confinement and exciton binding energy, thus enhancing spin polarization, especially in regions with a high excitation pump fluence based on the DP mechanism. In the case of low excitation pump fluence, the BAP mechanism dominates, as evidenced by the observed decrease in the polarization ratio from CP-SHG measurement. Using density functional theory analysis, we elucidate how the distinctive 8-coordination environment of lead bromide building blocks effectively suppresses spin–orbit coupling at the conduction band minimum. This suppression significantly diminishes spin-splitting, thereby slowing the spin relaxation rate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structural and optical properties of nanoparticles formed by laser ablation of porous silicon in liquids: Perspectives in biophotonics

The paper discusses the possibility of manufacturing silicon nanoparticles, which are suitable for contrasting biological tissues imaged by optical coherence tomography, by femtosecond laser ablation of porous silicon in various liquids. The manufactured nanoparticles are characterised by average sizes of 87, 112, and 102 nm for cases of ablation in water, ethanol, and liquid nitrogen, respectively, as well as a relatively narrow size distribution, which provides additional advantages for subsequent delivery into biological tissues. Electrochemical etching, which results in the formation of layers of porous silicon, allows the yield of ablation products to be increased several-fold by lowering the ablation threshold, thereby increasing the light scattering efficiency of the prepared suspensions compared with the case of using crystalline silicon as targets. The possibility of obtaining high-contrast images of a biotissue phantom based on an agar gel with embedded nanoparticles is shown. The magnitude of the contrast depends on the liquid used for ablation and correlates with the values of the reduced scattering coefficient of the studied suspensions. (paper)

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Scattered–light–sheet microscopy with sub–cellular resolving power

Since its first demonstration over 100 years ago, scattering-based light-sheet microscopy has recently re-emerged as a key modality in label-free tissue imaging and cellular morphometry; however, scattering-based light-sheet imaging with subcellular resolution remains an unmet target to date. This is because related approaches inevitably superimpose speckle or granular intensity modulation on to the native subcellular features. Here, we addressed this challenge by deploying a time-averaged pseudo-thermalized light-sheet illumination. While pseudo-thermalizing the illumination sheet increased its lateral dimensions, we achieved subcellular resolving power at ultralow irradiance levels after image deconvolution. We validated this approach by imaging cytosolic carbon depots in yeast and bacteria with increased specificity and no staining. Altogether, we expect this scattering-based light-sheet microscopy approach will advance live single-cell imaging investigations by conferring low-irradiance and label-free operation towards eradicating phototoxicity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Lattice light-sheet microscopy allows for super-resolution imaging of receptors in leaf tissue

Plant leaf tissues are difficult to image via fluorescent microscopy, largely due to the presence of chlorophyll and other pigments that provide large background fluorescence. An advantage of Lattice Light-Sheet microscopy is its use of Bessel beams that illuminate a thin focal region of interest for microscopy, allowing for the excitation of fluorescent molecules within this region without surrounding chlorophyll-like objects outside of the region of interest. Here, we apply STORM Super-resolution techniques to observe Receptor-Like Kinases in Arabidopsis thaliana leaf cells. By applying this technique with the Lattice Light-Sheet, we can localize immune response proteins in sub-100 nm length scales and reconstruct three-dimensional locations of proteins within individual leaf cells. Using this technique, we observed the effect of the elicitors ATP and flg22, where we observed a significant degree of internalization of cognate receptors P2K1 and FLS2. We were also able to similarly observe differences in colocalization due to stimulation with these elicitors, where we observe proteins on the membrane becoming less colocalized as a result of stimulation, suggesting an immune response mechanism involving receptors internalizing via pathways distinct to the receptor. Further, these data show the Lattice Light-Sheet’s capabilities for imaging tissue with problematic background fluorescence that otherwise makes super-resolution fluorescence microscopy difficult.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Fourier-based three-dimensional multistage transformer for aberration correction in multicellular specimens

High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. Although wavefront sensor-based adaptive optics (AO) can measure these aberrations, such hardware solutions are typically complex, expensive to implement and slow when serially mapping spatially varying aberrations across large fields of view. Here we introduce AOViFT (adaptive optical vision Fourier transformer)—a machine learning-based aberration sensing framework built around a three-dimensional multistage vision transformer that operates on Fourier domain embeddings. AOViFT infers aberrations and restores diffraction-limited performance in puncta-labeled specimens with substantially reduced computational cost, training time and memory footprint compared to conventional architectures or real-space networks. We validated AOViFT on live gene-edited zebrafish embryos, demonstrating its ability to correct spatially varying aberrations using either a deformable mirror or postacquisition deconvolution. By eliminating the need for the guide star and wavefront sensing hardware and simplifying the experimental workflow, AOViFT lowers technical barriers for high-resolution volumetric microscopy across diverse biological samples.

Alshaabi, Thayer [Howard Hughes Medical Institute,↗
DOE OSTI2025

Cryosectioning-enhanced super-resolution microscopy for single-protein imaging across cells and tissues

DNA-points accumulation for imaging in nanoscale topography (DNA-PAINT) enables nanoscale imaging with virtually unlimited multiplexing and molecular counting. Here, we address challenges, such as variable imaging performance and target accessibility, that can limit its broader applicability. Specifically, we enhance its capacity for robust single-protein imaging and molecular counting by optimizing the integration of total internal reflection fluorescence microscopy with physical sectioning, in particular, Tokuyasu cryosectioning. Our method, tomographic and kinetically enhanced DNA-PAINT (tkPAINT), achieves 3 nm localization precision across diverse samples, enhanced imager binding, and improved cellular integrity. tkPAINT can facilitate molecular counting with DNA-PAINT inside the nucleus, as demonstrated through its quantification of the in situ abundance of RNA Polymerase II in both HeLa cells as well as mouse tissues. Anticipating that tkPAINT could become a versatile tool for the exploration of biomolecular organization and interactions across cells and tissues, we also demonstrate its capacity to support multiplexing, multimodal targeting of proteins and nucleic acids, and three-dimensional (3D) imaging.

Science & Technology - Other Topics↗