Volumetric B-mode ultrasound and Doppler Imaging: Automatic Tracking With One Single Camera

Vascular diseases may occur in the upper extremities, and the lesions can span the entire length of the blood vessel. One of the most popular methods to identify vascular disorders is ultrasound Doppler imaging. However, traditional two-dimensional (2D) ultrasound Doppler imaging cannot capture the entire length of a long vessel in one image. Medical professionals often have to painstakingly reconstruct three-dimensional (3D) data using 2D ultrasound images to locate the lesions, especially for large blood vessels. 3D ultrasound Doppler imaging can display the morphological structure of blood vessels and the distribution of lesions more directly, providing a more comprehensive view compared to 2D imaging. In this work, we propose a wide-range 3D volumetric ultrasound Doppler imaging system with dual modality, in which a high-definition camera is adopted to automatically track the movement of the ultrasound transducer, simultaneously capturing a corresponding sequence of 2D ultrasound Doppler images. We conducted experiments on human arms using our proposed system and separately with X-ray computerized tomography (X-CT). The comparison results prove the potential value of our proposed system in the diagnosis of arm vascular diseases.

Rapid, high-contrast, and steady volumetric imaging with Bessel-beam-based two-photon fluorescence microscopy

Significance

Two-photon fluorescence microscopy (TPFM) excited by Gaussian beams requires axial tomographic scanning for three-dimensional (3D) volumetric imaging, which is a time-consuming process, and the slow imaging speed hinders its application for in vivo brain imaging. The Bessel focus, characterized by an extended depth of focus and constant resolution, facilitates the projection of a 3D volume onto a two-dimensional image, which significantly enhances the speed of volumetric imaging.

Aim

We aimed to demonstrate the ability of a TPFM with a sidelobe-free Bessel beam to provide a promising tool for research in live biological specimens.

Approach

Comparative in vivo imaging was conducted in live mouse brains and transgenic zebrafish to evaluate the performance of TPFM and Bessel-beam-based TPFM. Additionally, an image-difference method utilizing zeroth-order and third-order Bessel beams was introduced to effectively suppress background interference introduced by sidelobes.

Results

In comparison with traditional TPFM, the Bessel-beams-based TPFM demonstrated a 30-fold increase in imaging throughput and speed. Furthermore, the effectiveness of the image-difference method was validated in live biological specimens, resulting in a substantial enhancement of image contrast. Importantly, our TPFM with a sidelobe-free Bessel beam exhibited robustness against axial displacements, a feature of considerable value for in vivo experiments.

Conclusions

We achieved rapid, high-contrast, and robust volumetric imaging of the vasculature in live mouse brains and transgenic zebrafish using our TPFM with a sidelobe-free Bessel beam.

A second dimension of somatosensory system injury? Thalamic volume loss and neuropathic pain in adults with cerebral palsy and periventricular white matter injury

Objectives

Lemniscal (motor-related) and spinothalamic (neuropathic pain-related) somatosensory abnormalities affect different subsets of adults with cerebral palsy (CP). Lemniscal/motor abnormalities are associated with posterior thalamic radiation white matter disruption in individuals with CP and white matter injury. We tested the hypothesis that neuropathic pain symptoms in this population are rather associated with injury of the somatosensory (posterior group nuclei) thalamus.

Methods

In this cross-sectional study, communicative adults with CP and bilateral white matter injury and neurotypical control participants volunteered to self-report pain symptoms and undergo research MRI. Posterior group thalamic nuclei volume was computed and correlated against neuropathic pain scores.

Results

Participants with CP (n=6) had, on average, 24% smaller posterior group thalamic volumes (95% CI [10-39%]; corrected p=0.01) than control participants. More severe volume loss was correlated with more severe neuropathic pain scores (ρ=-0.87 [-0.99,-0.20]; p=0.02).

Discussion

Association with thalamic volume loss suggests that neuropathic pain in adults with CP may frequently be central neuropathic pain. Complementing assessments of white matter microstructure, regional brain volumes hold promise as diagnostic biomarkers for central neuropathic pain in individuals with structural brain disorders.

Recurrent and convolutional neural networks for sequential multispectral optoacoustic tomography (MSOT) imaging

Multispectral optoacoustic tomography (MSOT) is a beneficial technique for diagnosing and analyzing biological samples since it provides meticulous details in anatomy and physiology. However, acquiring high through-plane resolution volumetric MSOT is time-consuming. Here, we propose a deep learning model based on hybrid recurrent and convolutional neural networks to generate sequential cross-sectional images for an MSOT system. This system provides three modalities (MSOT, ultrasound, and optoacoustic imaging of a specific exogenous contrast agent) in a single scan. This study used ICG-conjugated nanoworms particles (NWs-ICG) as the contrast agent. Instead of acquiring seven images with a step size of 0.1 mm, we can receive two images with a step size of 0.6 mm as input for the proposed deep learning model. The deep learning model can generate five other images with a step size of 0.1 mm between these two input images meaning we can reduce acquisition time by approximately 71%.

Fluoropolymer Coated DNA Nanoclews for Volumetric Visualization of Oligonucleotides Delivery and Near Infrared Light Activated Anti-Angiogenic Oncotherapy

The potential of microRNA regulation in oncotherapy is limited by the lack of delivery vehicles. Herein, it is shown that fluoropolymer coated DNA nanoclews (FNCs) provide outstanding ability to deliver oligonucleotide through circulation and realize near infrared (NIR) light activated angiogenesis suppression to abrogate tumors. Oligonucleotides are loaded in DNA nanoclews through sequence specific bindings and then a fluorinated zwitterionic polymer is coated onto the surface of nanoclews. Further incorporating quantum dots in the polymer coating endows the vectors with NIR-IIb (1500-1700 nm) fluorescence and NIR light triggered release ability. The FNC vector can deliver oligonucleotides to cancer cells systemically and realize on-demand cytosolic release of the cargo with high transfection efficiency. Taking advantage of the NIR-IIb emission, the whole delivery process of FNCs is visualized volumetrically in vivo with a NIR light sheet microscope. Loaded by FNCs, an oligonucleotide can effectively silence the target miRNA when activated with NIR light, and inhibit angiogenesis inside tumor, leading to complete ablation of cancer. These findings suggest FNCs can be used as an efficient oligonucleotide delivery platform to modulate the expression of endogenous microRNA in gene therapy of cancer.

Optical single-pixel volumetric imaging by three-dimensional light-field illumination

Three-dimensional single-pixel imaging (3D SPI) has become an attractive imaging modality for both biomedical research and optical sensing. 3D-SPI techniques generally depend on time-of-flight or stereovision principle to extract depth information from backscattered light. However, existing implementations for these two optical schemes are limited to surface mapping of 3D objects at depth resolutions, at best, at the millimeter level. Here, we report 3D light-field illumination single-pixel microscopy (3D-LFI-SPM) that enables volumetric imaging of microscopic objects with a near-diffraction-limit 3D optical resolution. Aimed at 3D space reconstruction, 3D-LFI-SPM optically samples the 3D Fourier spectrum by combining 3D structured light-field illumination with single-element intensity detection. We build a 3D-LFI-SPM prototype that provides an imaging volume of ∼390 × 390 × 3,800 μm3 and achieves 2.7-μm lateral resolution and better than 37-μm axial resolution. Its capability of 3D visualization of label-free optical absorption contrast is demonstrated by imaging single algal cells in vivo. Our approach opens broad perspectives for 3D SPI with potential applications in various fields, such as biomedical functional imaging.

3D Chemical Imaging by Fluorescence-detected Mid-Infrared Photothermal Fourier Light Field Microscopy

Three-dimensional molecular imaging of living organisms and cells plays a significant role in modern biology. Yet, current volumetric imaging modalities are largely fluorescence-based and thus lack chemical content information. Mid-infrared photothermal microscopy as a chemical imaging technology provides infrared spectroscopic information at submicrometer spatial resolution. Here, by harnessing thermosensitive fluorescent dyes to sense the mid-infrared photothermal effect, we demonstrate 3D fluorescence-detected mid-infrared photothermal Fourier light field (FMIP-FLF) microscopy at the speed of 8 volumes per second and submicron spatial resolution. Protein contents in bacteria and lipid droplets in living pancreatic cancer cells are visualized. Altered lipid metabolism in drug-resistant pancreatic cancer cells is observed with the FMIP-FLF microscope.

Dynamic Volumetric Imaging of Mouse Cerebral Blood Vessels In Vivo with an Ultralong Anti-Diffracting Beam

Volumetric imaging of a mouse brain in vivo with one-photon and two-photon ultralong anti-diffracting (UAD) beam illumination was performed. The three-dimensional (3D) structure of blood vessels in the mouse brain were mapped to a two-dimensional (2D) image. The speed of volumetric imaging was significantly improved due to the long focal length of the UAD beam. Comparing one-photon and two-photon UAD beam volumetric imaging, we found that the imaging depth of two-photon volumetric imaging (80 μm) is better than that of one-photon volumetric imaging (60 μm), and the signal-to-background ratio (SBR) of two-photon volumetric imaging is two times that of one-photon volumetric imaging. Therefore, we used two-photon UAD volumetric imaging to perform dynamic volumetric imaging of mouse brain blood vessels in vivo, and obtained the blood flow velocity.

VoDEx: a Python library for time annotation and management of volumetric functional imaging data

In functional imaging studies, accurately synchronizing the time course of experimental manipulations and stimulus presentations with resulting imaging data is crucial for analysis. Current software tools lack such functionality, requiring manual processing of the experimental and imaging data, which is error-prone and potentially non-reproducible. We present VoDEx, an open-source Python library that streamlines the data management and analysis of functional imaging data. VoDEx synchronizes the experimental timeline and events (eg. presented stimuli, recorded behavior) with imaging data. VoDEx provides tools for logging and storing the timeline annotation, and enables retrieval of imaging data based on specific time-based and manipulation-based experimental conditions. Availability and Implementation: VoDEx is an open-source Python library and can be installed via the "pip install" command. It is released under a BSD license, and its source code is publicly accessible on GitHub https://github.com/LemonJust/vodex. A graphical interface is available as a napari-vodex plugin, which can be installed through the napari plugins menu or using "pip install." The source code for the napari plugin is available on GitHub https://github.com/LemonJust/napari-vodex.

High-resolution volumetric information fusion for depth of field enhancement in photoacoustic microscopy

Optical-resolution photoacoustic microscopy suffers from limited depth of field due to the strongly focused laser beam. Here, a novel volumetric information fusion is proposed to achieve large volumetric and high-resolution imaging. First, three-dimensional stationary wavelet transform was performed on the multi-focus data to obtain eight wavelet coefficients. Differential evolution based on joint weighted evaluation was then employed to optimize the block size of division for each wavelet coefficient. The proposed fusion rule using standard deviation for focus detection was used to fuse the corresponding sub-coefficients. Finally, photoacoustic imaging with large depth of field can be achieved by the inverse stationary wavelet transform. Performance test shows that the depth of field of photoacoustic imaging can be doubled without sacrificing lateral resolution. The proposed volumetric information fusion can further promote the capability of volumetric imaging of optical-resolution photoacoustic microscopy and will be helpful in the acquisition of physiological and pathological process.

Single-shot optical projection tomography for high-speed volumetric imaging of dynamic biological samples

A single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic biological samples is presented. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio, but the sequential acquisition of projection images typically requires samples to be immobilized during the acquisition. A proof-of-principle system capable of single-shot tomography of a ~1 mm3 volume is presented, demonstrating camera-limited rates of up to 62.5 volumes/s, which has been applied to 3D imaging of a freely swimming zebrafish embryo. This is achieved by recording eight projection views simultaneously on four low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under £5000. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including high throughput flow cytometry applied to model organisms and fluid dynamics studies.

Technical note: Performance evaluation of volumetric imaging based on motion modeling by principal component analysis

PURPOSE

To quantitatively evaluate the achievable performance of volumetric imaging based on lung motion modeling by principal component analysis (PCA).

METHODS

In volumetric imaging based on PCA, internal deformation was represented as a linear combination of the eigenvectors derived by PCA of the deformation vector fields evaluated from patient-specific four-dimensional-computed tomography (4DCT) datasets. The volumetric image was synthesized by warping the reference CT image with a deformation vector field which was evaluated using optimal principal component coefficients (PCs). Larger PCs were hypothesized to reproduce deformations larger than those included in the original 4DCT dataset. To evaluate the reproducibility of PCA-reconstructed volumetric images synthesized to be close to the ground truth as possible, mean absolute error (MAE), structure similarity index measure (SSIM) and discrepancy of diaphragm position were evaluated using 22 4DCT datasets of nine patients.

RESULTS

Mean MAE and SSIM values for the PCA-reconstructed volumetric images were approximately 80 HU and 0.88, respectively, regardless of the respiratory phase. In most test cases including the data of which motion range was exceeding that of the modeling data, the positional error of diaphragm was less than 5 mm. The results suggested that large deformations not included in the modeling 4DCT dataset could be reproduced. Furthermore, since the first PC correlated with the displacement of the diaphragm position, the first eigenvector became the dominant factor representing the respiration-associated deformations. However, other PCs did not necessarily change with the same trend as the first PC, and no correlation was observed between the coefficients. Hence, randomly allocating or sampling these PCs in expanded ranges may be applicable to reasonably generate an augmented dataset with various deformations.

CONCLUSIONS

Reasonable accuracy of image synthesis comparable to those in the previous research were shown by using clinical data. These results indicate the potential of PCA-based volumetric imaging for clinical applications.

Fast-spin-echo versus rapid gradient-echo for 3D magnetization-prepared acquisitions: Application to inhomogeneous magnetization transfer

PURPOSE

To evaluate the benefits of fast spin echo (FSE) imaging over rapid gradient-echo (RAGE) for magnetization-prepared inhomogeneous magnetization transfer (ihMT) imaging.

METHODS

A 3D FSE sequence was modified to include an ihMT preparation (ihMT-FSE) with an optional CSF suppression based on an inversion-recovery (ihMT-FLAIR). After numeric simulations assessing SNR benefits of FSE and the potential impact of an additional inversion-recovery, ihMT-RAGE, ihMT-FSE, and ihMT-FLAIR sequences were compared in a group of six healthy volunteers, evaluating image quality, thermal, and physiological noise as well as quantification using an ihMT saturation (ihMTsat) approach. A preliminary exploration in the cervical spinal cord was also conducted in a group of three healthy volunteers.

RESULTS

Several fold improvements in thermal SNR were observed with ihMT-FSE in agreement with numerical simulations. However, we observed significantly higher physiological noise in ihMT-FSE compared to ihMT-RAGE that was mitigated in ihMT-FLAIR, which provided the best total SNR (+74% and +49% compared to ihMT-RAGE in the white and gray matter, P ≤ 0.004). IhMTsat quantification was successful in all cases with strong correlation between all sequences (r2  > 0.75). Early experiments showed potential for spinal cord imaging.

CONCLUSIONS

FSE generally offers higher SNR compared to gradient-echo based acquisitions for magnetization-prepared contrasts as illustrated here in the case of ihMT. However, physiological noise has a significant effect, but an inversion-recovery-based CSF suppression was shown to be efficient in mitigating effects of CSF motion.

A novel design framework of synthetic radial aperture focusing for volumetric transrectal ultrasound imaging

In this paper, we present a novel design framework of synthetic radial aperture focusing for three-dimensional (3D) transrectal ultrasound imaging (TRUS-rSAF), in which multiple transmittance/reception events at different scanning angles are synthesized to reconstruct a radial plane in the target volume, securing high spatial resolution and texture uniformity. A theory-based design approach has not been available to push the envelope of the 3D rSAF technique. Herein, a closed-form analytical description of the TRUS-rSAF method is presented for the first time, effectively delineating spatial resolution and grating lobe positions in the radial dimension of a TRUS transducer. We demonstrate a solid optimization workflow based on the theoretical foundation to improve its spatiotemporal resolution, grating lobe artifacts, and signal-to-noise ratio. A specific design criterion was considered to outperform a clinical 3D TRUS imaging as a reference (TRUS-REF), where each radial plane is reconstructed with a single transmittance/reception event using a motorized actuator. The optimized TRUS-rSAF method significantly enhanced spatial resolution up to 50% over the TRUS-REF method while providing clinically effective temporal resolution (2-8 volume/sec) with negligible grating lobe artifacts. The results indicate that the proposed design approach would enable a novel TRUS imaging solution in clinics.

Higher-order regression three-dimensional motion-compensation method for real-time optical coherence tomography volumetric imaging of the cornea

SIGNIFICANCE

Optical coherence tomography (OCT) allows high-resolution volumetric three-dimensional (3D) imaging of biological tissues in vivo. However, 3D-image acquisition can be time-consuming and often suffers from motion artifacts due to involuntary and physiological movements of the tissue, limiting the reproducibility of quantitative measurements.

AIM

To achieve real-time 3D motion compensation for corneal tissue with high accuracy.

APPROACH

We propose an OCT system for volumetric imaging of the cornea, capable of compensating both axial and lateral motion with micron-scale accuracy and millisecond-scale time consumption based on higher-order regression. Specifically, the system first scans three reference B-mode images along the C-axis before acquiring a standard C-mode image. The difference between the reference and volumetric images is compared using a surface-detection algorithm and higher-order polynomials to deduce 3D motion and remove motion-related artifacts.

RESULTS

System parameters are optimized, and performance is evaluated using both phantom and corneal (ex vivo) samples. An overall motion-artifact error of <4.61 microns and processing time of about 3.40 ms for each B-scan was achieved.

CONCLUSIONS

Higher-order regression achieved effective and real-time compensation of 3D motion artifacts during corneal imaging. The approach can be expanded to 3D imaging of other ocular tissues. Implementing such motion-compensation strategies has the potential to improve the reliability of objective and quantitative information that can be extracted from volumetric OCT measurements.

Three-Dimensional H-Scan Ultrasound Imaging of Early Breast Cancer Response to Neoadjuvant Therapy in a Murine Model

OBJECTIVES

Three-dimensional (3D) H-scan is a new ultrasound (US) technique that images the relative size of acoustic scatterers. The goal of this research was to evaluate use of 3D H-scan US imaging for monitoring early breast cancer response to neoadjuvant therapy using a preclinical murine model of breast cancer.

MATERIALS AND METHODS

Preclinical studies were conducted using luciferase-positive breast cancer-bearing mice (n = 40). Anesthetized animals underwent US imaging at baseline before administration with an apoptosis-inducing drug or a saline control. Image data were acquired using a US scanner equipped with a volumetric transducer following either a shorter- or longer-term protocol. The later included bioluminescent imaging to quantify tumor cell viability. At termination, tumors were excised for ex vivo analysis.

RESULTS

In vivo results showed that 3D H-scan US imaging is considerably more sensitive to tumor changes after apoptosis-inducing drug therapy as compared with traditional B-scan US. Although there was no difference at baseline (P > 0.99), H-scan US results from treated tumors exhibited progressive decreases in image intensity (up to 62.2% by day 3) that had a significant linear correlation with cancer cell nuclear size (R2 > 0.51, P < 0.001). Results were validated by histological data and a secondary longitudinal study with survival as the primary end point.

DISCUSSION

Experimental results demonstrate that noninvasive 3D H-scan US imaging can detect an early breast tumor response to apoptosis-inducing drug therapy. Local in vivo H-scan US image intensity correlated with cancer cell nuclear size, which is one of the first observable changes of a cancer cell undergoing apoptosis and confirmed using histological techniques. Early imaging results seem to provide prognostic insight on longer-term tumor response. Overall, 3D H-scan US imaging is a promising technique that visualizes the entire tumor and detects breast cancer response at an early stage of therapy.

Two-stage deep learning network-based few-view image reconstruction for parallel-beam projection tomography

BACKGROUND

Projection tomography (PT) is a very important and valuable method for fast volumetric imaging with isotropic spatial resolution. Sparse-view or limited-angle reconstruction-based PT can greatly reduce data acquisition time, lower radiation doses, and simplify sample fixation modes. However, few techniques can currently achieve image reconstruction based on few-view projection data, which is especially important for in vivo PT in living organisms.

METHODS

A 2-stage deep learning network (TSDLN)-based framework was proposed for parallel-beam PT reconstructions using few-view projections. The framework is composed of a reconstruction network (R-net) and a correction network (C-net). The R-net is a generative adversarial network (GAN) used to complete image information with direct back-projection (BP) of a sparse signal, bringing the reconstructed image close to reconstruction results obtained from fully projected data. The C-net is a U-net array that denoises the compensation result to obtain a high-quality reconstructed image.

RESULTS

The accuracy and feasibility of the proposed TSDLN-based framework in few-view projection-based reconstruction were first evaluated with simulations, using images from the DeepLesion public dataset. The framework exhibited better reconstruction performance than traditional analytic reconstruction algorithms and iterative algorithms, especially in cases using sparse-view projection images. For example, with as few as two projections, the TSDLN-based framework reconstructed high-quality images very close to the original image, with structural similarities greater than 0.8. By using previously acquired optical PT (OPT) data in the TSDLN-based framework trained on computed tomography (CT) data, we further exemplified the migration capabilities of the TSDLN-based framework. The results showed that when the number of projections was reduced to 5, the contours and distribution information of the samples in question could still be seen in the reconstructed images.

CONCLUSIONS

The simulations and experimental results showed that the TSDLN-based framework has strong reconstruction abilities using few-view projection images, and has great potential in the application of in vivo PT.

Post hoc Correction of Chromatic Aberrations in Large-Scale Volumetric Images in Confocal Microscopy

Over the last decade, tissue-clearing techniques have expanded the scale of volumetric fluorescence imaging of the brain, allowing for the comprehensive analysis of neuronal circuits at a millimeter scale. Multicolor imaging is particularly powerful for circuit tracing with fluorescence microscopy. However, multicolor imaging of large samples often suffers from chromatic aberration, where different excitation wavelengths of light have different focal points. In this study, we evaluated chromatic aberrations for representative objective lenses and a clearing agent with confocal microscopy and found that axial aberration is particularly problematic. Moreover, the axial chromatic aberrations were often depth-dependent. Therefore, we developed a program that is able to align depths for different fluorescence channels based on reference samples with fluorescent beads or data from guide stars within biological samples. We showed that this correction program can successfully correct chromatic aberrations found in confocal images of multicolor-labeled brain tissues. Our simple post hoc correction strategy is useful to obtain large-scale multicolor images of cleared tissues with minimal chromatic aberrations.

Real-time CT image generation based on voxel-by-voxel modeling of internal deformation by utilizing the displacement of fiducial markers

PURPOSE

To show the feasibility of real-time CT image generation technique utilizing internal fiducial markers that facilitate the evaluation of internal deformation.

METHODS

In the proposed method, a linear regression model that can derive internal deformation from the displacement of fiducial markers is built for each voxel in the training process before the treatment session. Marker displacement and internal deformation are derived from the four-dimensional computed tomography (4DCT) dataset. In the treatment session, the three-dimensional deformation vector field is derived according to the marker displacement, which is monitored by the real-time imaging system. The whole CT image can be synthesized by deforming the reference CT image with a deformation vector field in real-time. To show the feasibility of the technique, image synthesis accuracy and tumor localization accuracy were evaluated using the dataset generated by extended NURBS-Based Cardiac-Torso (XCAT) phantom and clinical 4DCT datasets from six patients, containing 10 CT datasets each. In the validation with XCAT phantom, motion range of the tumor in training data and validation data were about 10 and 15 mm, respectively, so as to simulate motion variation between 4DCT acquisition and treatment session. In the validation with patient 4DCT dataset, eight CT datasets from the 4DCT dataset were used in the training process. Two excluded inhale CT datasets can be regarded as the datasets with large deformations more than training dataset. CT images were generated for each respiratory phase using the corresponding marker displacement. Root mean squared error (RMSE), normalized RMSE (NRMSE), and structural similarity index measure (SSIM) between the original CT images and the synthesized CT images were evaluated as the quantitative indices of the accuracy of image synthesis. The accuracy of tumor localization was also evaluated.

RESULTS

In the validation with XCAT phantom, the mean NRMSE, SSIM, and three-dimensional tumor localization error were 7.5 ± 1.1%, 0.95 ± 0.02, and 0.4 ± 0.3 mm, respectively. In the validation with patient 4DCT dataset, the mean RMSE, NRMSE, SSIM, and three-dimensional tumor localization error in six patients were 73.7 ± 19.6 HU, 9.2 ± 2.6%, 0.88 ± 0.04, and 0.8 ± 0.6 mm, respectively. These results suggest that the accuracy of the proposed technique is adequate when the respiratory motion is within the range of the training dataset. In the evaluation with a marker displacement larger than that of the training dataset, the mean RMSE, NRMSE, and tumor localization error were about 100 HU, 13%, and <2.0 mm, respectively, except for one case having large motion variation. The performance of the proposed method was similar to those of previous studies. Processing time to generate the volumetric image was <100 ms.

CONCLUSION

We have shown the feasibility of the real-time CT image generation technique for volumetric imaging.

In vivo dynamic 3D imaging of oocytes and embryos in the mouse oviduct

Developmental biologists have always relied on imaging to shed light on dynamic cellular events. However, processes such as mammalian fertilization and embryogenesis are generally inaccessible for direct imaging. In consequence, how the oviduct (fallopian tube) facilitates the transport of gametes and preimplantation embryos continues to be unanswered. Here we present a combination of intravital window and optical coherence tomography for dynamic, volumetric, in vivo imaging of oocytes and embryos as they are transported through the mouse oviduct. We observed location-dependent circling, oscillating, and long-distance bi-directional movements of oocytes and embryos that suggest regulatory mechanisms driving transport and question established views in the field. This in vivo imaging approach can be combined with a variety of genetic and pharmacological manipulations for live functional analysis, bringing the potential to investigate reproductive physiology in its native state.

Wang and Larina present in vivo volumetric imaging of oocytes and embryos as they are transported through the mouse oviduct with optical coherence tomography and an intravital microscopy. The study reveals complex dynamics of oocytes and embryos that suggest a regulatory role of cilia and oviductal contractions in driving the transport.

Perspective on fast-evolving photoacoustic tomography

SIGNIFICANCE

Acoustically detecting the rich optical absorption contrast in biological tissues, photoacoustic tomography (PAT) seamlessly bridges the functional and molecular sensitivity of optical excitation with the deep penetration and high scalability of ultrasound detection. As a result of continuous technological innovations and commercial development, PAT has been playing an increasingly important role in life sciences and patient care, including functional brain imaging, smart drug delivery, early cancer diagnosis, and interventional therapy guidance.

AIM

Built on our 2016 tutorial article that focused on the principles and implementations of PAT, this perspective aims to provide an update on the exciting technical advances in PAT.

APPROACH

This perspective focuses on the recent PAT innovations in volumetric deep-tissue imaging, high-speed wide-field microscopic imaging, high-sensitivity optical ultrasound detection, and machine-learning enhanced image reconstruction and data processing. Representative applications are introduced to demonstrate these enabling technical breakthroughs in biomedical research.

CONCLUSIONS

We conclude the perspective by discussing the future development of PAT technologies.

3D Whole-Brain Imaging Approaches to Study Brain Tumors

Simple Summary

Brain tumors integrate into the brain and consist of tumor cells with different molecular alterations. During brain tumor pathogenesis, a variety of cell types surround the tumors to either inhibit or promote tumor growth. These cells are collectively referred to as the tumor microenvironment. Three-dimensional and/or longitudinal visualization approaches are needed to understand the growth of these tumors in time and space. In this review, we present three imaging modalities that are suitable or that can be adapted to study the volumetric distribution of malignant or tumor-associated cells in the brain. In addition, we highlight the potential clinical utility of some of the microscopy approaches for brain tumors using exemplars from solid tumors.

Abstract

Although our understanding of the two-dimensional state of brain tumors has greatly expanded, relatively little is known about their spatial structures. The interactions between tumor cells and the tumor microenvironment (TME) occur in a three-dimensional (3D) space. This volumetric distribution is important for elucidating tumor biology and predicting and monitoring response to therapy. While static 2D imaging modalities have been critical to our understanding of these tumors, studies using 3D imaging modalities are needed to understand how malignant cells co-opt the host brain. Here we summarize the preclinical utility of in vivo imaging using two-photon microscopy in brain tumors and present ex vivo approaches (light-sheet fluorescence microscopy and serial two-photon tomography) and highlight their current and potential utility in neuro-oncology using data from solid tumors or pathological brain as examples.

Serial Block-Face Scanning Electron Microscopy (SBF-SEM) of Biological Tissue Samples

Serial block-face scanning electron microscopy (SBF-SEM) allows for the collection of hundreds to thousands of serially-registered ultrastructural images, offering an unprecedented three-dimensional view of tissue microanatomy. While SBF-SEM has seen an exponential increase in use in recent years, technical aspects such as proper tissue preparation and imaging parameters are paramount for the success of this imaging modality. This imaging system benefits from the automated nature of the device, allowing one to leave the microscope unattended during the imaging process, with the automated collection of hundreds of images possible in a single day. However, without appropriate tissue preparation cellular ultrastructure can be altered in such a way that incorrect or misleading conclusions might be drawn. Additionally, images are generated by scanning the block-face of a resin-embedded biological sample and this often presents challenges and considerations that must be addressed. The accumulation of electrons within the block during imaging, known as "tissue charging," can lead to a loss of contrast and an inability to appreciate cellular structure. Moreover, while increasing electron beam intensity/voltage or decreasing beam-scanning speed can increase image resolution, this can also have the unfortunate side effect of damaging the resin block and distorting subsequent images in the imaging series. Here we present a routine protocol for the preparation of biological tissue samples that preserves cellular ultrastructure and diminishes tissue charging. We also provide imaging considerations for the rapid acquisition of high-quality serial-images with minimal damage to the tissue block.

Comparative observer effects in 2D and 3D localization tasks

Purpose: Three-dimensional "volumetric" imaging methods are now a common component of medical imaging across many imaging modalities. Relatively little is known about how human observers localize targets masked by noise and clutter as they scroll through a 3D image and how it compares to a similar task confined to a single 2D slice. Approach: Gaussian random textures were used to represent noisy volumetric medical images. Subjects were able to freely inspect the images, including scrolling through 3D images as part of their search process. A total of eight experimental conditions were evaluated (2D versus 3D images, large versus small targets, power-law versus white noise). We analyze performance in these experiments using task efficiency and the classification image technique. Results: In 3D tasks, median response times were roughly nine times longer than 2D, with larger relative differences for incorrect trials. The efficiency data show a dissociation in which subjects perform with higher statistical efficiency in 2D tasks for large targets and higher efficiency in 3D tasks with small targets. The classification images suggest that a critical mechanism behind this dissociation is an inability to integrate across multiple slices to form a 3D localization response. The central slices of 3D classification images are remarkably similar to the corresponding 2D classification images. Conclusions: 2D and 3D tasks show similar weighting patterns between 2D images and the central slice of 3D images. There is relatively little weighting across slices in the 3D tasks, leading to lower task efficiency with respect to the ideal observer.

2.5D microscopy: Fast, high-throughput imaging via volumetric projection for quantitative subcellular analysis

Imaging-based single-cell analysis is essential to study the expression level and functions of biomolecules at subcellular resolution. However, its low throughput has prevented the measurement of numerous cellular features from multiples cells in a rapid and efficient manner. Here we report 2.5D microscopy that significantly improves the throughput of fluorescence imaging systems while maintaining high-resolution and single-molecule sensitivity. Instead of sequential z-scanning, volumetric information is projected onto a 2D image plane in a single shot by engineering the emitted fluorescence light. Our approach provides an improved imaging speed and uniform focal response within a specific imaging depth, which enabled us to perform quantitative single-molecule RNA measurements over a 2×2 mm2 region within an imaging depth of ~5 μm for mammalian cells in <10 min and immunofluorescence imaging at a >30 Hz volumetric frame rate with reduced photobleaching. Our microscope also offers the ability of multi-color imaging, depth control and super-resolution imaging.

A comparative study between high-definition volumetric imaging computed tomography and multi-slice computed tomography in the detection of acute thoraco-lumbar disc extrusions in dogs

Computed tomography (CT) is commonly used to image intervertebral disc extrusion (IVDE) in dogs. The current gold standard for CT imaging is the use of multi-slice CT (MS CT) units. Smaller high-definition volumetric imaging (HDVI) mobile CT has been marketed for veterinary practice. This unit is described as an advanced flat panel. The goal of this manuscript was to evaluate the ability of the HDVI CT in detecting IVDE without the need for CT myelography, compared with the detection of acute disc extrusions with a MS CT without the need for MS CT myelogram. Retrospective blinded analyses of 219 dogs presented for thoraco-lumbar IVDE that had a HDVI CT (n = 123) or MS CT (n = 96) were performed at a single referral hospital. A total of 123 cases had HDVI CT scans with surgically confirmed IVDE. The IVDE was identified in 88/123 (72%) dogs on pre-contrast HDVI CT. The remaining 35/128 (28%) cases required a HDVI CT myelogram to identify the IVDE. Ninety-six cases had MS CT scans with surgically confirmed IVDE. The IVDE was identified in 78/96 (81%) dogs on the pre-contrast MS CT. The remaining 18/96 (19%) cases had a MS CT myelogram to identify the IVDE. Multi-slice CT detected IVDE significantly more than HDVI CT (p = 0.032). This study showed that the ability of HDVI CT for detecting IVDE is lower than that of MS CT. The HDVI CT system may be useful in smaller referral practices, with a lower case load where space is limited.

Wide field-of-view volumetric imaging by a mesoscopic scanning oblique plane microscopy with switchable objective lenses

BACKGROUND

Conventional light sheet fluorescence microscopy (LSFM), or selective plane illumination microscopy (SPIM), enables high-resolution 3D imaging over a large volume by using two orthogonally aligned objective lenses to decouple excitation and emission. The recent development of oblique plane microscopy (OPM) simplifies LSFM design with only one single objective lens, by using off-axis excitation and remote focusing. However, most reports on OPM have a limited microscopic field of view (FOV), typically within 1×1 mm2. Our goal is to overcome the limitation with a new variant of OPM to achieve a mesoscopic FOV.

METHODS

We implemented an optical design of mesoscopic scanning OPM to allow the use of low numerical aperture (NA) objective lenses. The angle of the intermediate image before the remote focusing system was increased by a demagnification under Scheimpflug condition such that the light collecting efficiency in the remote focusing system was significantly improved. A telescope composed of cylindrical lenses was used to correct the distorted image caused by the demagnification design. We characterized the 3D resolutions and imaging volume by imaging fluorescent microspheres, and demonstrated the volumetric imaging on intact whole zebrafish larvae, mouse cortex, and multiple Caenorhabditis elegans (C. elegans).

RESULTS

We demonstrate a mesoscopic FOV up to ~6×5×0.6 mm3 volumetric imaging, the largest reported FOV by OPM so far. The angle of the intermediate image plane is independent of the magnification as long as the size of the pupil aperture of the objectives is the same. As a result, the system is highly versatile, allowing simple switching between different objective lenses with low (10×, NA 0.3) and median NA (20×, NA 0.5). Detailed microvasculature in zebrafish larvae, mouse cortex, and neurons in C. elegans are clearly visualized in 3D.

CONCLUSIONS

The proposed mesoscopic scanning OPM allows using low NA objectives such that centimeter-level FOV volumetric imaging can be achieved. With the extended FOV, simple sample mounting protocol, and the versatility of changeable FOVs/resolutions, our system will be ready for the varieties of applications requiring in vivo volumetric imaging over large length scales.

Recurrence and Coniglobus Volumetric Resolution of Subacute and Chronic Subdural Hematoma Post-Middle Meningeal Artery Embolization

Objective: To study the efficacy of middle meningeal artery (MMA) embolization for the treatment of chronic subdural hematoma (SDH) and characterize its post-embolization volumetric resolution. Methods: Ten patients diagnosed with 13 cSDH underwent MMA embolization. SDH volumes were measured from time of initial discovery on imaging to pre-operative, post-operative, short-term and long-term follow-up. Time between procedure to obliteration was also measured. Volumetric analysis was done using the coniglobus formula, and recurrence rate as well as resolution timeline was defined using best-fit models. Results: Out of 10 patients, five were recurrent lesions, three were bilateral and seven unilateral cSDH. Average and median pre-operative volumes were 105.3 cc and 97.4 cc, respectively. Embolization on average was performed 21 days after discovery. Sixty percent of patients had concurrent antiplatelets or anticoagulation use. Forty percent underwent embolization treatment as the primary therapy. Recurrence was not seen in any patients treated with embolization. There were no peri- or post-operative complications. Five patients experienced complete or near-complete obliteration, while those with partial resolution showed a composite average of 75% volumetric reduction in 45 days. Post-embolization, the volumetric resolution followed an exponential decay curve over time and was independent of initial volume. Conclusion: MMA embolization contributed to a marked reduction in SDH volume post-operatively and can be used as a curative therapy for primary or recurrent chronic SDH.

Machine Learning Driven Contouring of High-Frequency Four-Dimensional Cardiac Ultrasound Data

Automatic boundary detection of 4D ultrasound (4DUS) cardiac data is a promising yet challenging application at the intersection of machine learning and medicine. Using recently developed murine 4DUS cardiac imaging data, we demonstrate here a set of three machine learning models that predict left ventricular wall kinematics along both the endo- and epi-cardial boundaries. Each model is fundamentally built on three key features: (1) the projection of raw US data to a lower dimensional subspace, (2) a smoothing spline basis across time, and (3) a strategic parameterization of the left ventricular boundaries. Model 1 is constructed such that boundary predictions are based on individual short-axis images, regardless of their relative position in the ventricle. Model 2 simultaneously incorporates parallel short-axis image data into their predictions. Model 3 builds on the multi-slice approach of model 2, but assists predictions with a single ground-truth position at end-diastole. To assess the performance of each model, Monte Carlo cross validation was used to assess the performance of each model on unseen data. For predicting the radial distance of the endocardium, models 1, 2, and 3 yielded average R2 values of 0.41, 0.49, and 0.71, respectively. Monte Carlo simulations of the endocardial wall showed significantly closer predictions when using model 2 versus model 1 at a rate of 48.67%, and using model 3 versus model 2 at a rate of 83.50%. These finding suggest that a machine learning approach where multi-slice data are simultaneously used as input and predictions are aided by a single user input yields the most robust performance. Subsequently, we explore the how metrics of cardiac kinematics compare between ground-truth contours and predicted boundaries. We observed negligible deviations from ground-truth when using predicted boundaries alone, except in the case of early diastolic strain rate, providing confidence for the use of such machine learning models for rapid and reliable assessments of murine cardiac function. To our knowledge, this is the first application of machine learning to murine left ventricular 4DUS data. Future work will be needed to strengthen both model performance and applicability to different cardiac disease models.

FINGERPRINT SIGN OF THE HENLE FIBER LAYER

PURPOSE

To describe the appearance of concentric, fingerprint-like waves within the Henle fiber layer (HFL) using en face optical coherence tomography in patients with tractional pathologies of the retina.

METHODS

Retrospective analysis of six eyes of six patients imaged by optical coherence tomography with volumetric slabs positioned at the level of the HFL.

RESULTS

Optical coherence tomography data from six patients with tractional vitreoretinal pathology were reviewed. Concentric, fingerprint-like microwaves were visualized through en face optical coherence tomography in all six study eyes at the level of the HFL. This finding resembled the finding of HFL waves previously noted histopathologically from force exerted on this layer.

CONCLUSION

In retinal pathologies in which specific physical forces act on the retina, volumetric optical coherence tomography may permit visualization of en face concentric, fingerprint-like hyperreflective rings within the HFL. This "fingerprint sign" may represent a biomechanical consequence of traction on the retina and allow clinical decision making based on improved recognition of the existence of such traction.

Quantitative Bio-Imaging Tools to Dissect the Interplay of Membrane and Cytoskeletal Actin Dynamics in Immune Cells

Cellular function is reliant on the dynamic interplay between the plasma membrane and the actin cytoskeleton. This critical relationship is of particular importance in immune cells, where both the cytoskeleton and the plasma membrane work in concert to organize and potentiate immune signaling events. Despite their importance, there remains a critical gap in understanding how these respective dynamics are coupled, and how this coupling in turn may influence immune cell function from the bottom up. In this review, we highlight recent optical technologies that could provide strategies to investigate the simultaneous dynamics of both the cytoskeleton and membrane as well as their interplay, focusing on current and future applications in immune cells. We provide a guide of the spatio-temporal scale of each technique as well as highlighting novel probes and labels that have the potential to provide insights into membrane and cytoskeletal dynamics. The quantitative biophysical tools presented here provide a new and exciting route to uncover the relationship between plasma membrane and cytoskeletal dynamics that underlies immune cell function.

An open-hardware sample mounting solution for inverted light-sheet microscopes with large detection objective lenses

Implementations of light-sheet microscopes are often incompatible with standard methods of sample mounting. Light-sheet microscopy uses orthogonal illumination and detection to create a thin sheet of light which does not illuminate the sample outside of the depth of field of the detection axis. Typically, this configuration involves a pair of orthogonal objectives which constrains the positioning and length of cover slips in the range of the detection objective. Here, we present an open-hardware sample mounting system for light-sheet microscopes using large detection objectives, built using 3D printed components and demonstrate the chamber's efficacy on live biological samples in a custom light-sheet microscope. LAY DESCRIPTION: Implementations of light-sheet microscopes are often incompatible with standard methods of sample mounting. Light-sheet microscopy creates a thin sheet of light at a certain depth of field within a volumetric sample. Typically, this configuration involves a pair of orthogonal objectives which constrains the positioning of samples and sample-mounting apparatus in range of the detection objective. To overcome the limitations of this setup, we present an open-hardware sample mounting system for light-sheet microscopes using large detection objectives, built using 3D printed components and demonstrate the chamber's efficacy on live biological samples in a custom light-sheet microscope.

Multiple mechanisms underpin cerebral and cerebellar white matter deficits in Friedreich ataxia: The IMAGE-FRDA study

Friedreich ataxia is a progressive neurodegenerative disorder with reported abnormalities in cerebellar, brainstem, and cerebral white matter. White matter structure can be measured using in vivo neuroimaging indices sensitive to different white matter features. For the first time, we examined the relative sensitivity and relationship between multiple white matter indices in Friedreich ataxia to more richly characterize disease expression and infer possible mechanisms underlying the observed white matter abnormalities. Diffusion-tensor, magnetization transfer, and T1-weighted structural images were acquired from 31 individuals with Friedreich ataxia and 36 controls. Six white matter indices were extracted: fractional anisotropy, diffusivity (mean, axial, radial), magnetization transfer ratio (microstructure), and volume (macrostructure). For each index, whole-brain voxel-wise between-group comparisons and correlations with disease severity, onset age, and gene triplet-repeat length were undertaken. Correlations between pairs of indices were assessed in the Friedreich ataxia cohort. Spatial similarities in the voxel-level pattern of between-group differences across the indices were also assessed. Microstructural abnormalities were maximal in cerebellar and brainstem regions, but evident throughout the brain, while macroscopic abnormalities were restricted to the brainstem. Poorer microstructure and reduced macrostructural volume correlated with greater disease severity and earlier onset, particularly in peri-dentate nuclei and brainstem regions. Microstructural and macrostructural abnormalities were largely independent. Reduced fractional anisotropy was most strongly associated with axial diffusivity in cerebral tracts, and magnetization transfer in cerebellar tracts. Multiple mechanisms likely underpin white matter abnormalities in Friedreich ataxia, with differential impacts in cerebellar and cerebral pathways.

Developing a novel hyperspectral imaging cryomacrotome for whole body fluorescence imaging

The ability to directly measure whole-body fluorescence can enable tracking of labeled cells, metastatic spread, and drug bio-distribution. We describe the development of a new hyperspectral imaging whole body cryo-macrotome designed to acquire 3-D fluorescence volumes in large specimens (whole animals) at high resolution. The use of hyperspectral acquisition provides full spectra at every voxel, enabling spectral decoupling of multiple fluorohpores and autofluorescence. We present examples of tissue spectra and spectral fitting in a rodent glioma xenograft.

Design of a Volumetric Imaging Sequence Using a Vantage-256 Ultrasound Research Platform Multiplexed With a 1024-Element Fully Sampled Matrix Array

Ultrasound imaging using a matrix array allows real-time multi-planar volumetric imaging. To enhance image quality, the matrix array should provide fast volumetric ultrasound imaging with spatially consistent focusing in the lateral and elevational directions. However, because of the significantly increased data size, dealing with massive and continuous data acquisition is a significant challenge. We have designed an imaging acquisition sequence that handles volumetric data efficiently using a single 256-channel Verasonics ultrasound research platform multiplexed with a 1024-element matrix array. The developed sequence has been applied for building an ultrasonic pupilometer. Our results demonstrate the capability of the developed approach for structural visualization of an ex vivo porcine eye and the temporal response of the modeled eye pupil with moving iris at the volume rate of 30 Hz. Our study provides a fundamental ground for researchers to establish their own volumetric ultrasound imaging platform and could stimulate the development of new volumetric ultrasound approaches and applications.

Three-dimensional interventional photoacoustic imaging for biopsy needle guidance with a linear array transducer

Needle placement is important for many clinical interventions, such as tissue biopsy, regional anesthesia and drug delivery. It is essential to visualize the spatial position of the needle and the target tissue during the interventions using appropriate imaging techniques. Based on the contrast of optical absorption, photoacoustic imaging is well suited for the guidance of interventional procedures. However, conventional photoacoustic imaging typically provides two-dimensional (2D) slices of the region of interest and could only visualize the needle and the target when they are within the imaging plane of the probe at the same time. This requires great alignment skill and effort. To ease this problem, we developed a 3D interventional photoacoustic imaging technique by fast scanning a linear array ultrasound probe and stitching acquired image slices. in vivo sentinel lymph node biopsy experiment shows that the technique could precisely locate a needle and a sentinel lymph node in a tissue volume while a perfusion experiment demonstrates that the technique could visualize the 3D distribution of injected methylene blue dye underneath the skin at high temporal and spatial resolution. The proposed technique provides a practical way for photoacoustic image-guided interventions.

A prospective blinded comparison of second trimester fetal measurements by expert and novice readers using low-cost novice-acquired 3D volumetric ultrasound

RATIONALE AND OBJECTIVES

Two-dimensional (2D) ultrasound (US) is operator dependent, requiring operator skill and experience to selectively identify and record planes of interest for subsequent interpretation. This limits the utility of US in settings in which expert sonographers are unavailable. Three-dimensional (3D) US acquisition of an anatomic target, which enables reconstruction of any plane through the acquired volume, might reduce operator dependence by providing any desired image plane for interpretation, without identification of target planes of interest at the time of acquisition. We applied a low-cost 3DUS technology because of the wider potential application compared with dedicated 3DUS systems. We chose second trimester fetal biometric parameters for study because of their importance in maternal-fetal health globally. We hypothesized that expert and novice interpretations of novice-acquired 3D volumes would not differ from each other nor from expert measurements of expert-acquired 2D images, the clinical reference standard.

MATERIALS AND METHODS

This was a prospective, blinded, observational study. Expert sonographers blinded to 3DUS volumes acquired 2DUS images of second trimester fetuses from 32 subjects, and expert readers performed interpretation, during usual care. A novice sonographer blinded to other clinical data acquired oriented 3DUS image volumes of the same subjects on the same date. Expert readers blinded to other data assessed placental location (PL), fetal presentation (FP), and amniotic fluid volume (AFV) in novice-acquired 3D volumes. Novice and expert raters blinded to other data independently measured biparietal diameter (BPD), humerus length (HL), and femur length (FL) for each fetus from novice-acquired 3D volumes. Corresponding gestational age (GA) estimates were calculated. Inter-rater reliability of measurements and GAs (expert 3D versus expert 2D, novice 3D versus expert 2D, and expert 3D versus novice 3D) were assessed by intraclass correlation coefficient (ICC). Mean inter-rater measurement differences were analyzed using one-way ANOVA.

RESULTS

3D volume acquisition and reconstruction required mean 30.4 s (±5.7) and 70.0 s (±24.0), respectively. PL, FP, and AFV were evaluated from volumes for all subjects; mean time for evaluation was 16 s (±0.0). PL, FP, and AFV could be evaluated for all subjects. At least one biometric measurement was possible for 31 subjects (97%). Agreement between rater pairs for a composite of all measures was excellent (ICCs ≥ 0.95), and for individual measures was good to excellent (ICCs ≥ 0.75). Inter-rater differences were not significant (p > .05).

CONCLUSIONS

Expert and novice interpretations of novice-acquired 3DUS volumes of second trimester fetuses provided reliable biometric measures compared with expert interpretation of expert-acquired 2DUS images. 3DUS volume acquisition with a low-cost system may reduce operator dependence of ultrasound.

Two-Color Volumetric Imaging of Neuronal Activity of Cortical Columns

To capture the emergent properties of neural circuits, high-speed volumetric imaging of neural activity at cellular resolution is needed. Here, we introduce wavelength multiplexing to perform fast volumetric two-photon imaging of cortical columns (>2,000 neurons in 10 planes at 10 vol/s), using two different calcium indicators, an electrically tunable lens and a spatial light modulator. We image the activity of neuronal populations from layers 2/3 to 5 of primary visual cortex from awake mice, finding a lack of columnar structures in orientation responses and revealing correlations between layers which differ from trial to trial. We also simultaneously image functional correlations between presynaptic layer 1 axons and postsynaptic layer 2/3 neurons. Wavelength multiplexing enhances high-speed volumetric microscopy and can be combined with other optical multiplexing methods to easily boost imaging throughput.

Volumetric chemical imaging by clearing-enhanced stimulated Raman scattering microscopy

Three-dimensional visualization of tissue structures using optical microscopy facilitates the understanding of biological functions. However, optical microscopy is limited in tissue penetration due to severe light scattering. Recently, a series of tissue-clearing techniques have emerged to allow significant depth-extension for fluorescence imaging. Inspired by these advances, we develop a volumetric chemical imaging technique that couples Raman-tailored tissue-clearing with stimulated Raman scattering (SRS) microscopy. Compared with the standard SRS, the clearing-enhanced SRS achieves greater than 10-times depth increase. Based on the extracted spatial distribution of proteins and lipids, our method reveals intricate 3D organizations of tumor spheroids, mouse brain tissues, and tumor xenografts. We further develop volumetric phasor analysis of multispectral SRS images for chemically specific clustering and segmentation in 3D. Moreover, going beyond the conventional label-free paradigm, we demonstrate metabolic volumetric chemical imaging, which allows us to simultaneously map out metabolic activities of protein and lipid synthesis in glioblastoma. Together, these results support volumetric chemical imaging as a valuable tool for elucidating comprehensive 3D structures, compositions, and functions in diverse biological contexts, complementing the prevailing volumetric fluorescence microscopy.

Primed Track, high-fidelity lineage tracing in mouse pre-implantation embryos using primed conversion of photoconvertible proteins

Accurate lineage reconstruction of mammalian pre-implantation development is essential for inferring the earliest cell fate decisions. Lineage tracing using global fluorescence labeling techniques is complicated by increasing cell density and rapid embryo rotation, which hampers automatic alignment and accurate cell tracking of obtained four-dimensional imaging data sets. Here, we exploit the advantageous properties of primed convertible fluorescent proteins (pr-pcFPs) to simultaneously visualize the global green and the photoconverted red population in order to minimize tracking uncertainties over prolonged time windows. Confined primed conversion of H2B-pr-mEosFP-labeled nuclei combined with light-sheet imaging greatly facilitates segmentation, classification, and tracking of individual nuclei from the 4-cell stage up to the blastocyst. Using green and red labels as fiducial markers, we computationally correct for rotational and translational drift, reduce overall data size, and accomplish high-fidelity lineage tracing even for increased imaging time intervals – addressing major concerns in the field of volumetric embryo imaging.

A mouse embryo starts with one cell, which divides to create identical daughters that quickly start to multiply. Within three to four days, certain cells begin to specialize and take on specific roles. Scientists want to track these early events to understand how they give rise to an individual formed of huge numbers of cells organized in specialized tissues. To do so, researchers genetically manipulate embryos so that each cell produces fluorescent molecules that ‘glow’ under light. These embryos are grown inside a special microscope for several days. Images are taken regularly and then processed by specialized software that automatically tracks the fluorescent cells and their daughters over time. This helps reconstruct the history of each cell, and which structures they give rise to.

However, many embryos move and turn around between images, and so software packages often lose track of which cell was which. Taking images more frequently is not possible because each imaging event exposes the embryo to light, which can damage its fragile cells.

To address this problem, Welling, Mohr et al. made embryonic cells produce a special fluorescent marker, which is normally green but can be converted to red. Then, a technique known as primed conversion was used so that only one cell in a four-cell embryo would glow red. Welling, Mohr et al. designed a piece of software, baptized ‘primed Track’, that can use this red cell (and its daughters) to reorient the embryo during image analysis and reliably identify and match any mother cell to its daughters. The new approach means the experiments require fewer imaging events, but also fewer embryos because even the ones that move a lot can be studied. This should help scientists look into how early life processes give rise to specialized cells, and even explore the fate of cells in other tissues.

Whole-Cell, 3D, and Multicolor STED Imaging with Exchangeable Fluorophores

We demonstrate stimulated emission depletion (STED) microscopy of whole bacterial and eukaryotic cells using fluorogenic labels that reversibly bind to their target structure. A constant exchange of labels guarantees the removal of photobleached fluorophores and their replacement by intact fluorophores, thereby circumventing bleaching-related limitations of STED super-resolution imaging. We achieve a constant labeling density and demonstrate a fluorescence signal for long and theoretically unlimited acquisition times. Using this concept, we demonstrate whole-cell, 3D, multicolor, and live-cell STED microscopy.

High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging in vivo

Optical imaging has become a powerful tool for studying brains in vivo. The opacity of adult brains makes microendoscopy, with an optical probe such as a gradient index (GRIN) lens embedded into brain tissue to provide optical relay, the method of choice for imaging neurons and neural activity in deeply buried brain structures. Incorporating a Bessel focus scanning module into two-photon fluorescence microendoscopy, we extended the excitation focus axially and improved its lateral resolution. Scanning the Bessel focus in 2D, we imaged volumes of neurons at high-throughput while resolving fine structures such as synaptic terminals. We applied this approach to the volumetric anatomical imaging of dendritic spines and axonal boutons in the mouse hippocampus, and functional imaging of GABAergic neurons in the mouse lateral hypothalamus in vivo.

Acoustic characterization of a miniature matrix transducer for pediatric 3D transesophageal echocardiography

This paper presents the design, fabrication and characterization of a miniature PZT-on-CMOS matrix transducer for real-time pediatric 3-dimensional (3D) transesophageal echocardiography (TEE). This 3D TEE probe consists of a 32 × 32 array of PZT elements integrated on top of an Application Specific Integrated Circuit (ASIC). We propose a partitioned transmit/receive array architecture wherein the 8 × 8 transmitter elements, located at the centre of the array, are directly wired out and the remaining receive elements are grouped into 96 sub-arrays of 3 × 3 elements. The echoes received by these sub-groups are locally processed by micro-beamformer circuits in the ASIC that allow pre-steering up to ±37°. The PZT-on-CMOS matrix transducer has been characterized acoustically and has a centre frequency of 5.8 MHz, -6 dB bandwidth of 67%, a transmit efficiency of 6 kPa/V at 30 mm, and a receive dynamic range of 85 dB with minimum and maximum detectable pressures of 5 Pa and 84 kPa respectively. The properties are very suitable for a miniature pediatric real-time 3D TEE probe.

Probe-based three-dimensional confocal laser endomicroscopy of brain tumors: technical note

Background

Confocal laser endomicroscopy (CLE) is used during fluorescence-guided brain tumor surgery for intraoperative microscopy of tumor tissue with cellular resolution. CLE could augment and expedite intraoperative decision-making and potentially aid in diagnosis and removal of tumor tissue.

Objective

To describe an extension of CLE imaging modality that produces Z-stack images and three-dimensional (3D) pseudocolored volumetric images.

Materials and methods

Hand-held probe-based CLE was used to collect images from GL261-luc2 gliomas in C57BL/6 mice and from human brain tumor biopsies. The mice were injected with fluorescein sodium (FNa) before imaging. Patients received FNa intraoperatively, and biopsies were imaged immediately in the operating room. Some specimens were counterstained with acridine orange, acriflavine, or Hoechst and imaged on a benchtop confocal microscope. CLE images at various depths were acquired automatically, compiled, rendered into 3D volumes using Fiji software and reviewed by a neuropathologist and neurosurgeons.

Results

CLE imaging, Z-stack acquisition, and 3D image rendering were performed using 19 mouse gliomas and 31 human tumors, including meningiomas, gliomas, and pituitary adenomas. Volumetric images and Z-stacks provided additional information about fluorescence signal distribution, cytoarchitecture, and the course of abnormal vasculature.

Conclusion

3D and Z-stack CLE imaging is a unique new option for live intraoperative endomicroscopy of brain tumors. The 3D images afford an increased spatial understanding of tumor cellular architecture and visualization of related structures compared with two-dimensional images. Future application of specific fluorescent probes could benefit from this rapid in vivo imaging technology for interrogation of brain tumor tissue.

A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity

The mammalian brain is a densely interconnected network that consists of millions to billions of neurons. Decoding how information is represented and processed by this neural circuitry requires the ability to capture and manipulate the dynamics of large populations at high speed and high resolution over a large area of the brain. Although the use of optical approaches by the neuroscience community has rapidly increased over the past two decades, most microscopy approaches are unable to record the activity of all neurons comprising a functional network across the mammalian brain at relevant temporal and spatial resolutions. In this review, we survey the recent development in optical technologies for Ca2+ imaging in this regard and provide an overview of the strengths and limitations of each modality and its potential for scalability. We provide guidance from the perspective of a biological user driven by the typical biological applications and sample conditions. We also discuss the potential for future advances and synergies that could be obtained through hybrid approaches or other modalities.

Through-focus or volumetric type of optical imaging methods: a review

In recent years, the use of through-focus (TF) or volumetric type of optical imaging has gained momentum in several areas such as biological imaging, microscopy, adaptive optics, material processing, optical data storage, and optical inspection. We provide a review of basic TF optical methods highlighting their design, major unique characteristics, and application space.

Studying Axon-Astrocyte Functional Interactions by 3D Two-Photon Ca2+ Imaging: A Practical Guide to Experiments and "Big Data" Analysis

Recent advances in fast volumetric imaging have enabled rapid generation of large amounts of multi-dimensional functional data. While many computer frameworks exist for data storage and analysis of the multi-gigabyte Ca²⁺ imaging experiments in neurons, they are less useful for analyzing Ca²⁺ dynamics in astrocytes, where transients do not follow a predictable spatio-temporal distribution pattern. In this manuscript, we provide a detailed protocol and commentary for recording and analyzing three-dimensional (3D) Ca²⁺ transients through time in GCaMP6f-expressing astrocytes of adult brain slices in response to axonal stimulation, using our recently developed tools to perform interactive exploration, filtering, and time-correlation analysis of the transients. In addition to the protocol, we release our in-house software tools and discuss parameters pertinent to conducting axonal stimulation/response experiments across various brain regions and conditions. Our software tools are available from the Volterra Lab webpage at https://wwwfbm.unil.ch/dnf/group/glia-an-active-synaptic-partner/member/volterra-andrea-volterra in the form of software plugins for Image J (NIH)—a de facto standard in scientific image analysis. Three programs are available: MultiROI_TZ_profiler for interactive graphing of several movable ROIs simultaneously, Gaussian_Filter5D for Gaussian filtering in several dimensions, and Correlation_Calculator for computing various cross-correlation parameters on voxel collections through time.

Theoretical characterization of annular array as a volumetric optoacoustic ultrasound handheld probe

Optoacoustic ultrasound (OPUS) is a promising hybridized technique for simultaneous acquisition of functional and morphological data. The optical specificity of optoacoustic leverages the diagnostic aptitude of ultrasonography beyond anatomy. However, this integration has been rarely practiced for volumetric imaging. The challenge lies in the effective imaging probes that preserve the functionality of both modalities. The potentials of a sparse annular array for volumetric OPUS imaging are theoretically investigated. In order to evaluate and optimize the performance characteristics of the probe, series of analysis in the framework of system model matrix was carried out. The two criteria of voxel crosstalk and eigenanalysis have been employed to unveil information about the spatial sensitivity, aliasing, and number of definable spatial frequency components. Based on these benchmarks, the optimal parameters for volumetric handheld probe are determined. In particular, the number, size, and the arrangement of the elements and overall aperture dimension were investigated. The result of the numerical simulation suggests that the segmented-annular array of 128 negatively focused elements with 1λ  ×  20λ size, operating at 5-MHz central frequency showcases a good agreement with the physical requirement of both imaging systems. We hypothesize that these features enable a high-throughput volumetric passive/active ultrasonic imaging system with great potential for clinical applications.

Anthropomorphic model observer performance in three-dimensional detection task for low-contrast computed tomography

X-ray medical imaging is increasingly becoming three-dimensional (3-D). The dose to the population and its management are of special concern in computed tomography (CT). Task-based methods with model observers to assess the dose-image quality trade-off are promising tools, but they still need to be validated for real volumetric images. The purpose of the present work is to evaluate anthropomorphic model observers in 3-D detection tasks for low-contrast CT images. We scanned a low-contrast phantom containing four types of signals at three dose levels and used two reconstruction algorithms. We implemented a multislice model observer based on the channelized Hotelling observer (msCHO) with anthropomorphic channels and investigated different internal noise methods. We found a good correlation for all tested model observers. These results suggest that the msCHO can be used as a relevant task-based method to evaluate low-contrast detection for CT and optimize scan protocols to lower dose in an efficient way.