The cytoarchitectonic landscape revealed by deep learning method facilitated precise positioning in mouse neocortex.

Neocortex is a complex structure with different cortical sublayers and regions. However, the precise positioning of cortical regions can be challenging due to the absence of distinct landmarks without special preparation. To address this challenge, we developed a cytoarchitectonic landmark identification pipeline. The fluorescence micro-optical sectioning tomography method was employed to image the whole mouse brain stained by general fluorescent nucleotide dye. A fast 3D convolution network was subsequently utilized to segment neuronal somas in entire neocortex. By approach, the cortical cytoarchitectonic profile and the neuronal morphology were analyzed in 3D, eliminating the influence of section angle. And the distribution maps were generated that visualized the number of neurons across diverse morphological types, revealing the cytoarchitectonic landscape which characterizes the landmarks of cortical regions, especially the typical signal pattern of barrel cortex. Furthermore, the cortical regions of various ages were aligned using the generated cytoarchitectonic landmarks suggesting the structural changes of barrel cortex during the aging process. Moreover, we observed the spatiotemporally gradient distributions of spindly neurons, concentrated in the deep layer of primary visual area, with their proportion decreased over time. These findings could improve structural understanding of neocortex, paving the way for further exploration with this method.

Diffuse optical tomography for mapping cerebral hemodynamics and functional connectivity in delirium.

INTRODUCTION: Delirium is associated with mortality and new onset dementia, yet the underlying pathophysiology remains poorly understood. Development of imaging biomarkers has been difficult given the challenging nature of imaging delirious patients. Diffuse optical tomography (DOT) offers a promising approach for investigating delirium given its portability and three-dimensional capabilities. METHODS: Twenty-five delirious and matched non-delirious patients (n = 50) were examined using DOT, comparing cerebral oxygenation and functional connectivity in the prefrontal cortex during and after an episode of delirium. RESULTS: Total hemoglobin values were significantly decreased in the delirium group, even after delirium resolution. Functional connectivity between the dorsolateral prefrontal cortex and dorsomedial prefrontal cortex was strengthened post-resolution compared to during an episode; however, this relationship was still significantly weaker compared to controls. DISCUSSION: These findings highlight DOT's potential as an imaging biomarker to measure impaired cerebral oxygenation and functional dysconnectivity during and after delirium. Future studies should focus on the role of cerebral oxygenation in delirium pathogenesis and exploring the etiological link between delirium and dementias. HIGHLIGHTS: We developed a portable diffuse optical tomography (DOT) system for bedside three-dimensional functional neuroimaging to study delirium in the hospital. We implemented a novel DOT task-focused seed-based correlation analysis. DOT revealed decreased cerebral oxygenation and functional connectivity strength in the delirium group, even after resolution of delirium.

Functional hemodynamic imaging markers for the prediction of pathological outcomes in breast cancer patients treated with neoadjuvant chemotherapy.

Significance: Achieving pathologic complete response (pCR) after neoadjuvant chemotherapy (NACT) is a significant predictor of increased likelihood of survival in breast cancer patients. Early prediction of pCR is of high clinical value as it could allow personalized adjustment of treatment regimens in non-responding patients for improved outcomes. Aim: We aim to assess the association between hemoglobin-based functional imaging biomarkers derived from diffuse optical tomography (DOT) and the pathological outcome represented by pCR at different timepoints along the course of NACT. Approach: Twenty-two breast cancer patients undergoing NACT were enrolled in a multimodal DOT and X-ray digital breast tomosynthesis (DBT) imaging study in which their breasts were imaged at different compression levels. Logistic regressions were used to study the associations between DOT-derived imaging markers evaluated after the first and second cycles of chemotherapy, respectively, with pCR status determined after the conclusion of NACT at the time of surgery. Receiver operating characteristic curve analysis was also used to explore the predictive performance of selected DOT-derived markers. Results: Normalized tumor HbT under half compression was significantly lower in the pCR group compared to the non-pCR group after two chemotherapy cycles (p=0.042). In addition, the change in normalized tumor StO2 upon reducing compression from full to half mammographic force was identified as another potential indicator of pCR at an earlier time point, i.e., after the first chemo cycle (p=0.038). Exploratory predictive assessments showed that AUCs using DOT-derived functional imaging markers as predictors reach as high as 0.75 and 0.71, respectively, after the first and second chemo cycle, compared to AUCs of 0.50 and 0.53 using changes in tumor size measured on DBT and MRI. Conclusions: These findings suggest that breast DOT could be used to assist response assessment in women undergoing NACT, a critical but unmet clinical need, and potentially enable personalized adjustments of treatment regimens.

Mapping brain function in adults and young children during naturalistic viewing with high-density diffuse optical tomography.

Human studies of early brain development have been limited by extant neuroimaging methods. MRI scanners present logistical challenges for imaging young children, while alternative modalities like functional near-infrared spectroscopy have traditionally been limited by image quality due to sparse sampling. In addition, conventional tasks for brain mapping elicit low task engagement, high head motion, and considerable participant attrition in pediatric populations. As a result, typical and atypical developmental trajectories of processes such as language acquisition remain understudied during sensitive periods over the first years of life. We evaluate high-density diffuse optical tomography (HD-DOT) imaging combined with movie stimuli for high resolution optical neuroimaging in awake children ranging from 1 to 7 years of age. We built an HD-DOT system with design features geared towards enhancing both image quality and child comfort. Furthermore, we characterized a library of animated movie clips as a stimulus set for brain mapping and we optimized associated data analysis pipelines. Together, these tools could map cortical responses to movies and contained features such as speech in both adults and awake young children. This study lays the groundwork for future research to investigate response variability in larger pediatric samples and atypical trajectories of early brain development in clinical populations.

Imperfect refractive index matching in scanning laser optical tomography and a method for digital correction.

Significance: Scanning laser optical tomography (SLOT) is a volumetric multi-modal imaging technique that is comparable to optical projection tomography and computer tomography. Image quality is crucially dependent on matching the refractive indexes (RIs) of the sample and surrounding medium, but RI matching often requires some effort and is never perfect. Aim: Reducing the burden of RI matching between the immersion medium and sample in biomedical imaging is a challenging and interesting task. We aim at implementing a post processing strategy for correcting SLOT measurements that have errors caused by RI mismatch. Approach: To better understand the problems with poorly matched Ris, simulated SLOT measurements with imperfect RI matching of the sample and medium are performed and presented here. A method to correct distorted measurements was developed and is presented and evaluated. This method is then applied to a sample containing fluorescent polystyrene beads and a sample made of olydimethylsiloxane with embedded fluorescent nanoparticles. Results: From the simulations, it is evident that measurements with an RI mismatch larger than 0.02 and no correction yield considerably worse results compared to perfectly matched measurements. RI mismatches larger than 0.05 make it almost impossible to resolve finer details and structures. By contrast, the simulations imply that a measurement with an RI mismatch of up to 0.1 can still yield reasonable results if the presented correction method is applied. The experiments validate the simulated results for an RI mismatch of about 0.09. Conclusions: The method significantly improves the SLOT image quality for samples with imperfectly matched Ris. Although the absolutely best imaging quality will be achieved with perfect RI matching, these results pave the way for imaging in SLOT with RI mismatches while maintaining high image quality.

Real-time breast lesion classification combining diffuse optical tomography frequency domain data and BI-RADS assessment.

Ultrasound (US)-guided diffuse optical tomography (DOT) has demonstrated potential for breast cancer diagnosis, in which real-time or near real-time diagnosis with high accuracy is desired. However, DOT's relatively slow data processing and image reconstruction speeds have hindered real-time diagnosis. Here, we propose a real-time classification scheme that combines US breast imaging reporting and data system (BI-RADS) readings and DOT frequency domain measurements. A convolutional neural network is trained to generate malignancy probability scores from DOT measurements. Subsequently, these scores are integrated with BI-RADS assessments using a support vector machine classifier, which then provides the final diagnostic output. An area under the receiver operating characteristic curve of 0.978 is achieved in distinguishing between benign and malignant breast lesions in patient data without image reconstruction.

IR780-based diffuse fluorescence tomography for cancer detection.

IR780 iodide is a commercially available targeted near-infrared contrast agent for in vivo imaging and cancer photodynamic or photothermal therapy, whereas the accumulation, dynamics, and retention of IR780 in biological tissue, especially in tumor is still under-explored. Diffuse fluorescence tomography (DFT) can be used for localization and quantification of the three-dimensional distribution of NIR fluorophores. Herein, a homemade DFT imaging system combined with tumor-targeted IR780 was utilized for cancer imaging and pharmacokinetic evaluation. The aim of this study is to comprehensively assess the biochemical and pharmacokinetic characteristics of IR780 with the aid of DFT imaging. The optimal IR780 concentration (20 µg/mL) was achieved first. Subsequently, the good biocompatibility and cellar uptake of IR780 was demonstrated through the mouse acute toxic test and cell assay. In vivo, DFT imaging effectively identified various subcutaneous tumors and revealed the long-term retention of IR780 in tumors and rapid metabolism in the liver. Ex vivo imaging indicated IR780 was mainly concentrated in tumor and lung with significantly different from the distribution in other organs. DFT imaging allowed sensitive tumor detection and pharmacokinetic rates analysis. Simultaneously, the kinetics of IR780 in tumors and liver provided more valuable information for application and development of IR780.

AI-driven projection tomography with multicore fibre-optic cell rotation.

Optical tomography has emerged as a non-invasive imaging method, providing three-dimensional insights into subcellular structures and thereby enabling a deeper understanding of cellular functions, interactions, and processes. Conventional optical tomography methods are constrained by a limited illumination scanning range, leading to anisotropic resolution and incomplete imaging of cellular structures. To overcome this problem, we employ a compact multi-core fibre-optic cell rotator system that facilitates precise optical manipulation of cells within a microfluidic chip, achieving full-angle projection tomography with isotropic resolution. Moreover, we demonstrate an AI-driven tomographic reconstruction workflow, which can be a paradigm shift from conventional computational methods, often demanding manual processing, to a fully autonomous process. The performance of the proposed cell rotation tomography approach is validated through the three-dimensional reconstruction of cell phantoms and HL60 human cancer cells. The versatility of this learning-based tomographic reconstruction workflow paves the way for its broad application across diverse tomographic imaging modalities, including but not limited to flow cytometry tomography and acoustic rotation tomography. Therefore, this AI-driven approach can propel advancements in cell biology, aiding in the inception of pioneering therapeutics, and augmenting early-stage cancer diagnostics.

K-CapsNet: K-Nearest Neighbor Based Convolution Capsule Network for Cerenkov Luminescence Tomography Reconstruction.

Cerenkov luminescence tomography (CLT) has received significant attention as a promising imaging modality that can display the three-dimensional (3D) distribution of radioactive probes. However, the reconstruction of CLT suffers from severe ill-posed problem. It is difficult for traditional model-based method to obtain satisfactory result. Recently, deep learning-based method have shown great potential for accurate and efficient CLT reconstruction. In this study, a KNN-based convolution capsule network, named K-CapsNet, is proposed for cerenkov luminescence tomography. In K-CapsNet, the surface photon intensity is encoded in capsule form. The KNN-based convolution and K-means clustering are proposed for efficient encoding. Numerical simulation experiments have been carried out to verify the performance of K-CapsNet, and the results show that it performs superior in source localization and morphological restoration compared with existing methods.

FISTA-NET: Deep Algorithm Unrolling for Cerenkov luminescence tomography.

Cerenkov luminescence tomography (CLT) is a highly sensitive and promising imaging technique that can be used to reconstruct the three-dimensional distribution of radioactive probes in living animals. However, the accuracy of CLT reconstruction is limited by the simplified radiative transfer equation and ill-conditioned inverse problem. To address this issue, we propose a model-based deep learning network that combines the neural network with a model-based approach to enhance the performance of CLT reconstruction. The Fast Iterative Shrinkage Thresholding Algorithm (FISTA), a traditional model-based approach, is expanded into a deep network (known as FISTA-NET). Each layer in the network represents an iteration of the algorithm steps, and connecting these layers can form a deep neural network. In addition, different from the traditional FISTA, the key parameters in FISTA, such as gradient step size and threshold value, can be learned through training data without manual production. To evaluate the performance of FISTA-NET, numerical simulation experiments were conducted, which demonstrate its excellent positioning and shape recovery abilities.Clinical Relevance-This indicates that FISTA-NET strategy can significantly improve the quality of CLT reconstruction, which is further beneficial to the assessment of disease activity and treatment effect based on CLT.

One-dimensional convolutional neural network for Jacobian in Diffuse Optical Tomography.

Non-linear least square minimization algorithms are often employed to solve Diffuse Optical Tomography (DOT) inverse problem. However, it is time-consuming to calculate the Jacobian matrix. This work has proposed a data-driven neural network method to improve computational efficiency. The singular value decomposition is employed to compute the updated Jacobian and a mapping from boundary measurements to the singular values based on a convolutional neural network (CNN) is learned to obtain the singular values. The method is validated with 3D numerical simulation data. We have demonstrated that the approach can save computation time compared to Adjoint method, and reconstructed absorption coefficient close to Adjoint method.Clinical Relevance- These results are not focused on clinical relevance currently, but in the future may be helpful to accelerant DOT reconstruction in clinic.

Imaging Cerebral Blood Vessels Using Near-Infrared Optical Tomography: A Simulation Study.

Cerebral veins have received increasing attention due to their importance in preoperational planning and the brain oxygenation measurement. There are different modalities to image those vessels, such as magnetic resonance angiography (MRA) and recently, contrast-enhanced (CE) 3D gradient-echo sequences. However, the current techniques have certain disadvantages, i.e., the long examination time, the requirement of contrast agents or inability to measure oxygenation. Near-infrared optical tomography (NIROT) is emerging as a viable new biomedical imaging modality that employs near infrared light (650-950 nm) to image biological tissue. It was proven to easily penetrate the skull and therefore enables the brain vessels to be assessed. NIROT utilizes safe non-ionizing radiation and can be applied in e.g., early detection of neonatal brain injury and ischemic strokes. The aim is to develop non-invasive label-free dynamic time domain (TD) NIROT to image the brain vessels. A simulation study was performed with the software (NIRFAST) which models light propagation in tissue with the finite element method (FEM). Both a simple shape mesh and a real head mesh including all the segmented vessels from MRI images were simulated using both FEM and a hybrid FEM-U-Net network, we were able to visualize the superficial vessels with NIROT with a Root Mean Square Error (RMSE) lower than 0.079.

Cross-scale tracing of nanoparticles and tumors at the single-cell level using the whole-lung atlas.

Currently, the effectiveness of oncotherapy is limited by tumor heterogeneities, which presents a huge challenge for the development of nanotargeted drug delivery systems (DDSs). Therefore, it is important to resolve the spatiotemporal interactions between tumors and nanoparticles. However, targeting evaluation has been limited by particle visualization due to the gap between whole-organ scale and subcellular precision. Here, a high-precision three-dimensional (3D) visualization of tumor structure based on the micro-optical sectioning tomography (MOST) system and fluorescence MOST (fMOST) system is presented to clarify 3D spatial distribution of nanoparticles within the tumor. We demonstrate that through the MOST/fMOST system, it is possible to reveal multidimensional and cross-scale correlations between the tumor structure and nanoparticle distribution to remodel the tumor microenvironment and explore the structural parameters of vasculature. This visualization methodology provides an accurate assessment of the efficacy, distribution, and targeting efficiency of DDSs for oncotherapy compared to available approaches.

Application of fluorescence micro-optical sectioning tomography in the cerebrovasculature and applicable vascular labeling methods.

Fluorescence micro-optical sectioning tomography (fMOST) is a three-dimensional (3d) imaging method at the mesoscopic level. The whole-brain of mice can be imaged at a high resolution of 0.32 × 0.32 × 1.00 µm3. It is useful for revealing the fine morphology of intact organ tissue, even for positioning the single vessel connected with a complicated vascular network across different brain regions in the whole mouse brain. Featuring its 3d visualization of whole-brain cross-scale connections, fMOST has a vast potential to decipher brain function and diseases. This article begins with the background of fMOST technology including a widespread 3D imaging methods comparison and the basic technical principal illustration, followed by the application of fMOST in cerebrovascular research and relevant vascular labeling techniques applicable to different scenarios.

Diffuse optical tomography spatial prior for EEG source localization in human visual cortex.

Electroencephalography (EEG) and diffuse optical tomography (DOT) are imaging methods which are widely used for neuroimaging. While the temporal resolution of EEG is high, the spatial resolution is typically limited. DOT, on the other hand, has high spatial resolution, but the temporal resolution is inherently limited by the slow hemodynamics it measures. In our previous work, we showed using computer simulations that when using the results of DOT reconstruction as the spatial prior for EEG source reconstruction, high spatio-temporal resolution could be achieved. In this work, we experimentally validate the algorithm by alternatingly flashing two visual stimuli at a speed that is faster than the temporal resolution of DOT. We show that the joint reconstruction using both EEG and DOT clearly resolves the two stimuli temporally, and the spatial confinement is drastically improved in comparison to reconstruction using EEG alone.

Single-exposure ultrasound-modulated optical tomography with a quaternary phase encoded mask.

Ultrasound-modulated optical tomography (UOT) is a deep-tissue imaging modality that provides optical contrast with acoustic resolution. Among existing implementations, camera-based UOT improves modulation depth through parallel detection but suffers from a low camera frame rate. The condition prohibits this technique from being applied to in vivo applications where speckles decorrelate on a time scale of 1 ms or less. To overcome this challenge, we developed single-exposure camera-based UOT by employing a quaternary phase encoded mask (QPEM). As a proof of concept, we demonstrated imaging of an absorptive target buried inside a dynamic scattering medium with a speckle correlation time as short as 0.49 ms, typical of living biological tissues. Benefiting from the QPEM-enabled single-exposure wavefront measurement (5.5 ms) and GPU-assisted wavefront reconstruction (0.97 ms), the point scanning and result update speed can reach up to 150 Hz. We envision that the QPEM-enabled single-exposure scheme paves the way for in vivo UOT imaging, which holds promise for a variety of medical and biological applications.

Three-dimensional label-free visualization of the interactions of PM2.5 with macrophages and epithelial cells using optical diffraction tomography.

Particulate matter ≤ 2.5 µm (PM2.5) poses health risks related to various diseases and infections. However, the interactions between PM2.5 and cells such as uptake and cell responses have not been fully investigated despite advances in bioimaging techniques, because the heterogeneous morphology and composition of PM2.5 make it challenging to employ labeling techniques, such as fluorescence. In this work, we visualized the interaction between PM2.5 and cells using optical diffraction tomography (ODT), which provides quantitative phase images by refractive index distribution. Through ODT analysis, the interactions of PM2.5 with macrophages and epithelial cells, such as intracellular dynamics, uptake, and cellular behavior, were successfully visualized without labeling techniques. ODT analysis clearly shows the behavior of phagocytic macrophages and nonphagocytic epithelial cells for PM2.5. Moreover, ODT analysis could quantitatively compare the accumulation of PM2.5 inside the cells. PM2.5 uptake by macrophages increased substantially over time, but uptake by epithelial cells increased only marginally. Our findings indicate that ODT analysis is a promising alternative approach to visually and quantitatively understanding the interaction of PM2.5 with cells. Therefore, we expect ODT analysis to be employed to investigate the interactions of materials and cells that are difficult to label.

Mapping cortical activations underlying covert and overt language production using high-density diffuse optical tomography.

Gold standard neuroimaging modalities such as functional magnetic resonance imaging (fMRI), positron emission tomography (PET), and more recently electrocorticography (ECoG) have provided profound insights regarding the neural mechanisms underlying the processing of language, but they are limited in applications involving naturalistic language production especially in developing brains, during face-to-face dialogues, or as a brain-computer interface. High-density diffuse optical tomography (HD-DOT) provides high-fidelity mapping of human brain function with comparable spatial resolution to that of fMRI but in a silent and open scanning environment similar to real-life social scenarios. Therefore, HD-DOT has potential to be used in naturalistic settings where other neuroimaging modalities are limited. While HD-DOT has been previously validated against fMRI for mapping the neural correlates underlying language comprehension and covert (i.e., "silent") language production, HD-DOT has not yet been established for mapping the cortical responses to overt (i.e., "out loud") language production. In this study, we assessed the brain regions supporting a simple hierarchy of language tasks: silent reading of single words, covert production of verbs, and overt production of verbs in normal hearing right-handed native English speakers (n = 33). First, we found that HD-DOT brain mapping is resilient to movement associated with overt speaking. Second, we observed that HD-DOT is sensitive to key activations and deactivations in brain function underlying the perception and naturalistic production of language. Specifically, statistically significant results were observed that show recruitment of regions in occipital, temporal, motor, and prefrontal cortices across all three tasks after performing stringent cluster-extent based thresholding. Our findings lay the foundation for future HD-DOT studies of imaging naturalistic language comprehension and production during real-life social interactions and for broader applications such as presurgical language assessment and brain-machine interfaces.

Unrolled-DOT: an interpretable deep network for diffuse optical tomography.

Significance: Imaging through scattering media is critical in many biomedical imaging applications, such as breast tumor detection and functional neuroimaging. Time-of-flight diffuse optical tomography (ToF-DOT) is one of the most promising methods for high-resolution imaging through scattering media. ToF-DOT and many traditional DOT methods require an image reconstruction algorithm. Unfortunately, this algorithm often requires long computational runtimes and may produce lower quality reconstructions in the presence of model mismatch or improper hyperparameter tuning. Aim: We used a data-driven unrolled network as our ToF-DOT inverse solver. The unrolled network is faster than traditional inverse solvers and achieves higher reconstruction quality by accounting for model mismatch. Approach: Our model "Unrolled-DOT" uses the learned iterative shrinkage thresholding algorithm. In addition, we incorporate a refinement U-Net and Visual Geometry Group (VGG) perceptual loss to further increase the reconstruction quality. We trained and tested our model on simulated and real-world data and benchmarked against physics-based and learning-based inverse solvers. Results: In experiments on real-world data, Unrolled-DOT outperformed learning-based algorithms and achieved over 10× reduction in runtime and mean-squared error, compared to traditional physics-based solvers. Conclusion: We demonstrated a learning-based ToF-DOT inverse solver that achieves state-of-the-art performance in speed and reconstruction quality, which can aid in future applications for noninvasive biomedical imaging.

Optical imaging of the small intestine immune compartment across scales.

The limitations of 2D microscopy constrain our ability to observe and understand tissue-wide networks that are, by nature, 3-dimensional. Optical projection tomography (OPT) enables the acquisition of large volumes (ranging from micrometres to centimetres) in various tissues. We present a multi-modal workflow for the characterization of both structural and quantitative parameters of the mouse small intestine. As proof of principle, we evidence its applicability for imaging the mouse intestinal immune compartment and surrounding mucosal structures. We quantify the volumetric size and spatial distribution of Isolated Lymphoid Follicles (ILFs) and quantify the density of villi throughout centimetre-long segments of intestine. Furthermore, we exhibit the age and microbiota dependence for ILF development, and leverage a technique that we call reverse-OPT for identifying and homing in on regions of interest. Several quantification capabilities are displayed, including villous density in the autofluorescent channel and the size and spatial distribution of the signal of interest at millimetre-scale volumes. The concatenation of 3D imaging with reverse-OPT and high-resolution 2D imaging allows accurate localisation of ROIs and adds value to interpretations made in 3D. Importantly, OPT may be used to identify sparsely-distributed regions of interest in large volumes whilst retaining compatibility with high-resolution microscopy modalities, including confocal microscopy. We believe this pipeline to be approachable for a wide-range of specialties, and to provide a new method for characterisation of the mouse intestinal immune compartment.