This research was supported in part through computational resources and services provided by Advanced Research Computing at the University of British Columbia, and by a University of British Columbia Department of Radiology AI Grant. RLE was supported by a Michael Smith Health Research BC Trainee Award.

The imaging cases shown here were approved by the University of British Columbia Providence Health Care Research Ethics Board (REB# H21-01237, H21-02149, H22-01264). Participants provided written informed consent prior to completing imaging. The overall pipeline from image acquisition to registration is outlined in Figure 2, and the protocol details here focus on the MR-CT image registration only. Image acquisition and segmentation are dependent on available or preferred imaging hardware, imaging protocols, and image analysis software tools and, therefore, are left to readers&#39; preference. The protocol is designed to be agnostic to those prior steps using single-label masks of the lungs following image segmentation.
1. Software setup
<ol>
	<li>Download and install ANTsPy (see Table of Materials), the Python wrapper for the Advanced Normalization Tools image processing library47,48,49. Tutorials are available at the link under the &#39;tutorials&#39; tab. ANTsPy is also available for Docker installation if desired. 
	NOTE: ANTsPy requires a Linux-based operating system or environment. For the examples here, ANTsPy was installed and used in a virtual high-performance computing environment on a local workstation. The protocol has tended to work better using a virtual computing environment in the authors&#39; experience.</li>
	<li>Download and install segmentation and/or visualization software of choice. 
	NOTE: For the present study, ITK-SNAP was used for visualization (see Table of Materials).</li>
	<li>Download and save the reg.py script (Supplementary File 1).</li>
</ol>
2. Image pre-processing
<ol>
	<li>Click to open images and masks in the desired image visualization software to verify image and mask orientation matches for all CT, 1H, and 129Xe files. Depending on the segmentation method and/or software used, the orientation of some images or masks may need to be adjusted. As needed, we recommend adjusting 1H and 129Xe images and mask orientation to match that of the native CT image.</li>
	<li>Save the image DICOMs and single-label masks (adjusted as in step 2.1 as needed) as Neuroimaging Informatics Technology Initiative files (NIfTI, *.nii; six files total) using the preferred software tool, in the same folder as reg.py that is accessible to the location where ANTsPy is installed and will be run. Follow the naming conventions as mentioned below.
	<ol>
		<li>1H MRI: Proton.nii; 1H MRI mask: Proton_mask.nii. 
		NOTE: Use the 1H image and mask after registration to 129Xe.</li>
		<li>129Xe MRI: Ventilation.nii; 129Xe MRI mask: Ventilation_mask.nii</li>
		<li>CT: CT.nii; CT mask: CT_mask.nii. 
		NOTE: The file names are hard-coded into the registration script and, therefore, must follow the mentioned format, or be revised in the script to match the desired naming convention. These steps can be completed together using any of the recommended software tools listed in step 1.2. With respect to those software tools, some will write the required header information automatically when saving .nii files, whereas others require additional steps to copy and write the header information.</li>
	</ol>
	</li>
</ol>
3. CT-XeMRI registration
<ol>
	<li>Open the reg.py file in the desired Python computing environment setup in step 1.1. 
	NOTE: Script reg.py is based on the built-in ANTs registration tools; additional documentation is available55.</li>
	<li>If using a virtual environment, set the number of central processing units (CPU), number threads, and RAM as desired or available in the computing environment. A virtual computing environment with 16 CPU, 1 thread per CPU, and 186 GB of available RAM was used for the examples herein.</li>
	<li>Set desired transformation and interpolation. The SyNAggro transformation with linear interpolation for images and generic label interpolation for single-label masks, which are default in the provided reg.py script, were&#160;used here. 
	NOTE: SyNAggro is a symmetric normalization transformation, which includes affine + deformable transformation plus more aggressive registration using fine-scale matching and more deformation (compared with plain SyN). Alternative transformation and interpolation algorithms are listed in the ANTs registration documentation link in step 3.155.</li>
	<li>Set the fixed and the moving image. Here, the&#160;CT (single-label mask) was set as the fixed image, and the&#160;1H MRI (single-label mask) was set as the moving image.</li>
	<li>Run reg.py in the Python computing environment. Full registration may take 5-10 min (using our parameters) or longer, depending on computing resources used or available. When complete, warped files will be automatically saved in the same directory as the original image files with the file names as follows: Proton_warped.nii.gz; Ventilation_warped.nii.gz; Ventilation_label_warped.nii.gz. 
	NOTE: NIfTI *.nii.gz files are just zipped versions of *.nii files and can be unzipped or opened as desired. Script reg.py can be modified as desired, for example, using different transformation or interpolation methods or mapping to or creating file directories.</li>
</ol>
4. Evaluation of registration results
<ol>
	<li>Open the CT.nii image as the base image in the desired visualization software.</li>
	<li>Open Ventilation_warped.nii.gz or Ventilation_label_warped.nii.gz as another image and overlay on the CT image with the desired color map.</li>
	<li>Review the overlap of the 129Xe image or mask with the CT image in all image planes (coronal, axial, sagittal), evaluating the visual alignment of landmarks such as the carina and lung boundaries (where available in the 129Xe image).</li>
	<li>Check the results. If satisfied with the results, registration is complete. 
	NOTE: The registered 129Xe image/mask can be multiplied by the CT mask to remove the trachea and main airways (if not removed prior to MRI segmentation) and remove any signal that falls outside of the CT lung boundaries after registration. Further quantification for regional structure-function measurements can be performed as desired.</li>
	<li>If not satisfied with the results, evaluate and optimize alternative types of transformation and associated parameters as needed.</li>
</ol>

RLE receives personal consulting fees from VIDA Diagnostics Inc. outside the submitted work. JAL has received an institutional grant from GE Healthcare and honoraria for lectures from Philips and GE Healthcare outside the submitted work.

CT and 129Xe MRI provide complementary information to evaluate regional lung structure and function that is best facilitated using image registration. Multi-modal image registration can be non-trivial to implement, and so the protocol provided here is intended to provide the tools for readers to register 129Xe MRI to CT. The provided protocol uses ANTsPy for easier implementation for users with a broad range of image processing experience using Python rather than C++, as in conventional ANTs. Overal...

Hyperpolarized gas magnetic resonance imaging (MRI) first emerged as a novel functional pulmonary imaging modality to evaluate pulmonary ventilation distribution nearly three decades ago1. Since then, research studies using hyperpolarized gas MRI have revealed numerous insights into the nature of lung function in patients with chronic lung diseases such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis2,3,4,5,6. Both hyperpolarized 3He and 129Xe gas have been used historically; however, 129Xe is now the primary inhaled agent because of the limited availability of 3He gas. 129Xe also freely diffuses across the alveolar membrane and is absorbed by red blood cells in the pulmonary capillaries; in this so-called &#39;dissolved phase,&#39; 129Xe resonates at unique frequencies that allow for measurement of regional gas exchange in a single breath-hold scan4,7,8. For quantification, volume-matched anatomical 1H MR images are typically contemporaneously acquired for co-registration with 129Xe to delineate boundaries of the thoracic cavity. Conventional 1H MRI, though, does not provide further lung structural information. The impetus for clinical translation of hyperpolarized 129Xe MRI grew in recent years with UK NHS approval in 2015 and US FDA approval in late 20225,9, yet advanced structural characterization is still mostly missing from the pulmonary MRI arsenal.
Chest computed tomography (CT) remains the mainstay of clinical imaging assessment of the lungs, providing three-dimensional high-resolution images of lung structure using conventional imaging protocols. Quantitative approaches have enabled rapid and repeatable measurement of parenchymal integrity, such as emphysema and interstitial lung abnormalities, large airway morphology and pulmonary vasculature, and regional anatomic characterization by identification and segmentation of lung lobes10,11. In the research space, quantitative CT has been widely used to better understand structural alterations and their relationships with patient outcomes in asthma and COPD in large observational studies such as the Severe Asthma Research Program (SARP)12, Genetic Epidemiology of COPD (COPDGene)13, Subpopulations and Intermediate Outcomes in COPD Study (SPIROMICS)14, Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-points (ECLIPSE)15, and Canadian Cohort of Obstructive Lung Disease (CanCOLD)16. Alternative CT methods such as expiratory imaging17,18 or computational models19 may derive functional information, but these methods are indirect, and conventional CT does not otherwise provide much for functional characterization of the lungs.
Taken together, CT and 129Xe MRI provide complementary lung structure-function information that can be exploited for regional analysis using image registration. Lung lobes identified on CT have allowed for lobar characterization of MRI ventilation patterns in asthma20,21,22, COPD23,24, bronchiectasis25, and lung cancer26,27. MRI ventilation abnormalities in asthma have also been directly spatially matched to abnormally remodeled large airways28,29,30,31 and air trapping indicative of small airways dysfunction20,32 measured on CT, and to probe regional treatment responses following whole-lung bronchial thermoplasty33. In COPD, MRI ventilation abnormalities have been linked to small airway dysfunction in milder diseases and emphysema in more severe diseases34,35,36. Beyond ventilation imaging in obstructive lung disease, heterogeneous spatial relationships between CT interstitial lung abnormalities and 129Xe MRI gas exchange patterns have also been demonstrated in idiopathic pulmonary fibrosis37. Such studies have provided a deeper understanding of regional lung structure-function in a range of lung diseases that can be used to inform future image-guided interventions.
Direct registration of anatomic CT and functional hyperpolarized gas MRI is challenging,&#160;however, due to fundamentally different imaging contrast between the two methods, the absence of hyperpolarized gas signal in regions of ventilation abnormalities, and potentially different lung volumes. Figure 1 shows four examples of 129Xe and paired anatomical 1H MRI and CT in a healthy volunteer (Figure 1A) and three participants with chronic obstructive pulmonary disease (COPD; Figure 1B-D), highlighting heterogeneous 129Xe ventilation patterns and varying missing lung boundaries in the COPD cases. The key to overcoming these challenges has been using the anatomical 1H MRI acquired contemporaneously with hyperpolarized gas MRI as an intermediate step to register hyperpolarized gas MRI to CT indirectly34,38. Early work employed side-by-side visual comparison and manual segmentation of CT structures, such as lung lobes, onto MRI space20. Advancements in computational resources and open-source image processing tools have enabled three-dimensional registration of CT and hyperpolarized gas MRI, for example, using modality independent neighborhood descriptor (MIND)23,30,34,39,40,41 or Advanced Normalization Toolkit (ANTs) registration21,22,27,31,32,37,38,42,43, both of which were top performers in a pulmonary image registration challenge44. One novel method coupled the two registrations rather than treating them independently45, which has been implemented in a full pulmonary image analysis pipeline designed for phenotyping lung disease46. Overall, hyperpolarized gas MRI to CT registration accuracy was improved using the intermediate 1H step38 and using deformable approaches over affine-only approaches38,45.
The goal here is to build from the existing literature and provide a protocol for 129Xe MR to CT image registration using open-source platforms47,48,49. The protocol is implemented using ANTsPy, and, in line with previous work38, registers a single-label lung mask from 1H MRI to the single-label lung mask from CT; the resulting transformation is subsequently applied to the 129Xe image to map it to the CT image space. The protocol outlined is intended to be appropriate for research or clinical settings, where applicable, and&#160;hyperpolarized 129Xe MRI is available.
For context, image acquisition and analysis for the examples provided herein were performed as follows. Chest CT was acquired at full inspiration (total lung capacity, TLC) according to an established low-dose research protocol50 with parameters: 64 x 0.625 collimation, 120 peak kilovoltage, tube current 100 mA, 0.5 s revolution time, spiral pitch 1.0, 1.25 mm slice thickness, 0.80 mm slice spacing, standard reconstruction kernel, display field-of-view limited to the most lateral extents of the lungs (to maximize spatial resolution). CT segmentation and analysis were performed using commercial software (see Table of Materials).
129Xe and volume-matched 1H MRI were performed according to published guidelines9. For full MRI acquisition details and protocol, readers are directed to another article in this collection51. MRI segmentation and registration were performed using a semi-automated custom pipeline using k-means clustering for 129Xe segmentation, seeded-region growing for 1H segmentation, and landmark-based affine registration to map the 1H image to the 129Xe image52. Affine registration is typically sufficient for 1H-129Xe MR registration to account for most lung inflation or patient position differences between acquisitions; deformable registration is typically not necessary. The 1H-129Xe registration step can be eliminated with simultaneously acquired 129Xe and 1H MRI in the same breath-hold53,54.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>3D Slicer</td>
			<td>Brigham and Women&#39;s Hospital (BWH)</td>
			<td>https://www.slicer.org/</td>
			<td>Image analysis/visualization software; open source</td>
		</tr>
		<tr>
			<td>ANTsPy</td>
			<td>NA</td>
			<td>https://github.com/ANTsX/ANTsPy</td>
			<td>Coding infrastructure; open source</td>
		</tr>
		<tr>
			<td>ITK-SNAP</td>
			<td>NA</td>
			<td>http://www.itksnap.org/pmwiki/pmwiki.php</td>
			<td>Image analysis/visualization software; open source</td>
		</tr>
		<tr>
			<td>MAGNETOM Vida 3.0T MRI</td>
			<td>Siemens Healthineers</td>
			<td>NA</td>
			<td>Can be any 1.5 T or 3.0 T scanner with broadband imaging capability</td>
		</tr>
		<tr>
			<td>MATLAB</td>
			<td>Mathworks</td>
			<td>https://www.mathworks.com/products/matlab.html</td>
			<td>General software, good for image analysis; available by subscription</td>
		</tr>
		<tr>
			<td>reg.py</td>
			<td>NA</td>
			<td>NA</td>
			<td>Registration script (Supplementary File 1)</td>
		</tr>
		<tr>
			<td>Revolution HD CT scanner</td>
			<td>GE Healthcare</td>
			<td>NA</td>
			<td>Can be any CT scanner with &#8805;64 detectors</td>
		</tr>
		<tr>
			<td>VIDA Insights</td>
			<td>VIDA Diagnostics Inc.</td>
			<td>NA</td>
			<td>CT analysis software; can be any to generate masks</td>
		</tr>
	</tbody>
</table>

multi-modal pulmonary imaging: using complementary information from ct and hyperpolarized 129xe mri to evaluate lung structure-function

Hyperpolarized 129Xe gas MRI is an emerging technique to evaluate and measure regional lung function including pulmonary gas distribution and gas exchange. Chest computed tomography (CT) still remains the clinical gold standard for imaging of the lungs, though, in part due to the rapid CT protocols that acquire high-resolution images in seconds and the widespread availability of CT scanners. Quantitative approaches have enabled the extraction of structural lung parenchymal, airway and vascular measurements from chest CT that have been evaluated in many clinical research studies. Together, CT and 129Xe MRI provide complementary information that can be used to evaluate regional lung structure and function, resulting in new insights into lung health and disease. 129Xe MR-CT image registration can be performed to measure regional lung structure-function to better understand lung disease pathophysiology, and to perform image-guided pulmonary interventions. Here, a method for 129Xe MRI-CT registration is outlined to support implementation in research or clinical settings. Registration methods and applications that have been employed to date in the literature are also summarized, and suggestions are provided for future directions that may further overcome technical challenges related to 129Xe MR-CT image registration and facilitate broader implementation of regional lung structure-function evaluation.

This study prospectively acquired paired CT and 129Xe MRI in a research setting for regional lung structure-function characterization and image-guided bronchoscopy across a range of lung diseases and conditions. Figure 3 shows registered 129Xe MRI ventilation and CT in coronal and sagittal planes for four representative participants with a range of MRI ventilation patterns (for the same participants of Figure 1). The registered 129</su...

Read this Scientific Article Protocol about Multi-modal Pulmonary Imaging: Using Complementary Information from CT and Hyperpolarized 129Xe MRI to Evaluate Lung Structure-Function at JoVE.com

Multi-modal Pulmonary Imaging: Using Complementary Information from CT and Hyperpolarized 129Xe MRI to Evaluate Lung Structure-Function

CT and 129Xe MRI provide complementary lung structure-function information that can be exploited for regional analysis using image registration. Here, we provide a protocol that builds from the existing literature for 129Xe MR to CT image registration using open-source platforms.

Multi-modal Pulmonary Imaging: Using Complementary Information from CT and Hyperpolarized 129Xe MRI to Evaluate Lung Structure-Function

Hyperpolarized 129Xe gas MRI is an emerging technique to evaluate and measure regional lung function including pulmonary gas distribution and gas ...

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495 Views.  St. Paul’s Hospital. CT and 129Xe MRI provide complementary lung structure-function information that can be exploited for regional analysis using image registration. Here, we provide a protocol that builds from the existing literature for 129Xe MR to CT image registration using open-source platforms.

Video: Multi-modal Pulmonary Imaging: Using Complementary Information from CT and Hyperpolarized 129Xe MRI to Evaluate Lung Structure-Function

Bronchial Thermoplasty:  A Novel Therapeutic Approach to Severe Asthma

Bronchial thermoplasty is a non-drug procedure for severe persistent asthma that delivers thermal energy to the airway wall in a precisely controlled manner to reduce excessive airway smooth muscle. Reducing airway smooth muscle decreases the ability of the airways to constrict, thereby reducing the frequency of asthma attacks. Bronchial thermoplasty is delivered by the Alair System and is performed in three outpatient procedure visits, each scheduled approximately three weeks apart. The first procedure treats the airways of the right lower lobe, the second treats the airways of the left lower lobe and the third and final procedure treats the airways in both upper lobes. After all three procedures are performed the bronchial thermoplasty treatment is complete.
Bronchial thermoplasty is performed during bronchoscopy with the patient under moderate sedation. All accessible airways distal to the mainstem bronchi between 3 and 10 mm in diameter, with the exception of the right middle lobe, are treated under bronchoscopic visualization. Contiguous and non-overlapping activations of the device are used, moving from distal to proximal along the length of the airway, and systematically from airway to airway as described previously. Although conceptually straightforward, the actual execution of bronchial thermoplasty is quite intricate and procedural duration for the treatment of a single lobe is often substantially longer than encountered during routine bronchoscopy. As such, bronchial thermoplasty should be considered a complex interventional bronchoscopy and is intended for the experienced bronchoscopist. Optimal patient management is critical in any such complex and longer duration bronchoscopic procedure. This article discusses the importance of careful patient selection, patient preparation, patient management, procedure duration, postoperative care and follow-up to ensure that bronchial thermoplasty is performed safely.
Bronchial thermoplasty is expected to complement asthma maintenance medications by providing long-lasting asthma control and improving asthma-related quality of life of patients with severe asthma. In addition, bronchial thermoplasty has been demonstrated to reduce severe exacerbations (asthma attacks) emergency rooms visits for respiratory symptoms, and time lost from work, school and other daily activities due to asthma.

Bronchial thermoplasty is a non-drug procedure for severe persistent asthma that delivers thermal energy to the airway wall in a precisely controlled manner to reduce excessive airway smooth muscle. Reducing airway smooth muscle decreases the ability of the airways to constrict, thereby reducing the frequency of asthma attacks.

Bronchial thermoplasty is a non-drug procedure for severe persistent asthma that delivers thermal energy to the airway wall in a precisely controlled ...

Multi-modal Imaging of Angiogenesis in a Nude Rat Model of Breast Cancer Bone Metastasis Using Magnetic Resonance Imaging, Volumetric Computed Tomography and Ultrasound

Angiogenesis is an essential feature of cancer growth and metastasis formation. In bone metastasis, angiogenic factors are pivotal for tumor cell proliferation in the bone marrow cavity as well as for interaction of tumor and bone cells resulting in local bone destruction. Our aim was to develop a model of experimental bone metastasis that allows in vivo assessment of angiogenesis in skeletal lesions using non-invasive imaging techniques.
For this purpose, we injected 105 MDA-MB-231 human breast cancer cells into the superficial epigastric artery, which precludes the growth of metastases in body areas other than the respective hind leg1. Following 25-30 days after tumor cell inoculation, site-specific bone metastases develop, restricted to the distal femur, proximal tibia and proximal fibula1. Morphological and functional aspects of angiogenesis can be investigated longitudinally in bone metastases using magnetic resonance imaging (MRI), volumetric computed tomography (VCT) and ultrasound (US).
MRI displays morphologic information on the soft tissue part of bone metastases that is initially confined to the bone marrow cavity and subsequently exceeds cortical bone while progressing. Using dynamic contrast-enhanced MRI (DCE-MRI) functional data including regional blood volume, perfusion and vessel permeability can be obtained and quantified2-4. Bone destruction is captured in high resolution using morphological VCT imaging. Complementary to MRI findings, osteolytic lesions can be located adjacent to sites of intramedullary tumor growth. After contrast agent application, VCT angiography reveals the macrovessel architecture in bone metastases in high resolution, and DCE-VCT enables insight in the microcirculation of these lesions5,6. US is applicable to assess morphological and functional features from skeletal lesions due to local osteolysis of cortical bone. Using B-mode and Doppler techniques, structure and perfusion of the soft tissue metastases can be evaluated, respectively. DCE-US allows for real-time imaging of vascularization in bone metastases after injection of microbubbles7.
In conclusion, in a model of site-specific breast cancer bone metastases multi-modal imaging techniques including MRI, VCT and US offer complementary information on morphology and functional parameters of angiogenesis in these skeletal lesions.

In the pathogenesis of bone metastasis, angiogenesis is a crucial process and therefore represents a target for imaging and therapy. Here, we present a rat model of site-specific breast cancer bone metastasis and describe strategies to non-invasively image angiogenesis in vivo using magnetic resonance imaging, volumetric computed tomography and ultrasound.

Angiogenesis is an essential feature of cancer growth and metastasis formation. In bone metastasis, angiogenic factors are pivotal for tumor cell ...

Angiogenesis in the Ischemic Rat Lung

The adult lung is perfused by both the systemic bronchial artery and the entire venous return flowing through the pulmonary arteries. In most lung pathologies, it is the smaller systemic vasculature that responds to a need for enhanced lung perfusion and shows robust neovascularization. Pulmonary vascular ischemia induced by pulmonary artery obstruction has been shown to result in rapid systemic arterial angiogenesis in man as well as in several animal models. Although the histologic assessment of the time course of bronchial artery proliferation in rats was carefully described by Weibel 1, mechanisms responsible for this organized growth of new vessels are not clear. We provide surgical details of inducing left pulmonary artery ischemia in the rat that leads to bronchial neovascularization. Quantification of the extent of angiogenesis presents an additional challenge due to the presence of the two vascular beds within the lung. Methods to determine functional angiogenesis based on labeled microsphere injections are provided.

The lung is perfused by both the systemic bronchial artery and pulmonary arteries. In most lung pathologies, it is the smaller systemic vasculature that shows robust neovascularization. Cessation of pulmonary blood flow promotes brisk bronchial angiogenesis. We provide surgical details of inducing left pulmonary artery ischemia that promotes bronchial neovascularization.

The  adult lung is perfused by both the systemic bronchial artery and the entire  venous return flowing through the pulmonary arteries. In most lung ...

A Multi-Modal Approach to Assessing Recovery in Youth Athletes Following Concussion

Concussion is one of the most commonly reported injuries amongst children and youth involved in sport participation. Following a concussion, youth can experience a range of short and long term neurobehavioral symptoms (somatic, cognitive and emotional/behavioral) that can have a significant impact on one&#8217;s participation in daily activities and pursuits of interest (e.g., school, sports, work, family/social life, etc.). Despite this, there remains a paucity in clinically driven research aimed specifically at exploring concussion within the youth sport population, and more specifically, multi-modal approaches to measuring recovery. This article provides an overview of a novel and multi-modal approach to measuring recovery amongst youth athletes following concussion. The presented approach involves the use of both pre-injury/baseline testing and post-injury/follow-up testing to assess performance across a wide variety of domains (post-concussion symptoms, cognition, balance, strength, agility/motor skills and resting state heart rate variability). The goal of this research is to gain a more objective and accurate understanding of recovery following concussion in youth athletes (ages 10-18 years). Findings from this research can help to inform the development and use of improved approaches to concussion management and rehabilitation specific to the youth sport community.

This article provides an overview of a multi-modal approach to assessing recovery following concussion in youth athletes. The described protocol uses pre- and post-concussion assessment of performance across a wide variety of domains and can inform the development of improved concussion rehabilitation protocols specific to the youth sport community.

Concussion is one of the most commonly reported injuries amongst children and youth involved in sport participation. Following a concussion, youth can ...

Real-time X-ray Imaging of Lung Fluid Volumes in Neonatal Mouse Lung

At birth, the lung undergoes a profound phenotypic switch from secretion to absorption, which allows for adaptation to breathing independently. Promoting and sustaining this phenotype is critically important in normal alveolar growth and gas exchange throughout life. Several in vitro studies have characterized the role of key regulatory proteins, signaling molecules, and steroid hormones that can influence the rate of lung fluid clearance. However, in vivo examinations must be performed to evaluate whether these regulatory factors play important physiological roles in regulating perinatal lung liquid absorption. As such, the utilization of real time X-ray imaging to determine perinatal lung fluid clearance, or pulmonary edema, represents a technological advancement in the field. Herein, we explain and illustrate an approach to assess the rate of alveolar lung fluid clearance and alveolar flooding in C57BL/6 mice at post natal day 10 using X-ray imaging and analysis. Successful implementation of this protocol requires prior approval from institutional animal care and use committees (IACUC), an in vivo small animal X-ray imaging system, and compatible molecular imaging software.

We present a protocol to assess the rate of alveolar fluid clearance or pulmonary edema in neonatal mouse lung using X-ray imaging technology.

At birth, the lung undergoes a profound phenotypic switch from secretion to absorption, which allows for adaptation to breathing independently. Promoting ...

Combining Volumetric Capnography And Barometric Plethysmography To Measure The Lung Structure-function Relationship

Tools to measure lung and airways volume are critical for pulmonary researchers interested in evaluating the impact of disease or novel therapies on the lung. Barometric plethysmography is a classic technique to evaluate the lung volume with a long history of clinical use. Volumetric capnography utilizes the profile of exhaled carbon dioxide to determine the volume of the conducting airways, or dead space, and provides an index of airways homogeneity. These techniques may be used independently, or in combination to evaluate the dependence of airways volume and homogeneity on lung volume. This paper provides detailed technical instructions to replicate these techniques and our representative data demonstrates that the airways volume and homogeneity are highly correlated to lung volume. We also provide a macro for the analysis of capnographic data, which can be modified or adapted to fit different experimental designs. The advantage of these measures is that their advantages and limitations are supported by decades of experimental data, and they can be made repeatedly in the same subject without expensive imaging equipment or technically advanced analysis algorithms. These methods may be particularly useful for investigators interested in perturbations that change both the functional residual capacity of the lung and airways volume.

Here, we describe two measures of pulmonary function &#8211; barometric plethysmography, which allows the measurement of lung volume, and volumetric capnography, a tool to measure the anatomic dead space and airways uniformity. These techniques may be used independently or combined to assess airways function at different lung volumes.

Tools to measure lung and airways volume are critical for pulmonary researchers interested in evaluating the impact of disease or novel therapies on the ...

Multi-Modal Home Sleep Monitoring in Older Adults

The gold standard for sleep monitoring is attended in-lab polysomnography; however, this method may be cost-prohibitive and inconvenient for patients and research participants. Home sleep testing has gained momentum in the field of sleep medicine due to its convenience and lower cost, as well as being more naturalistic. The accuracy and quality of home sleep testing, however, may be variable because studies are not monitored by sleep technologists. There has been some success in improving the accuracy of home sleep studies by having trained sleep technicians assist participants inside their homes with putting on the devices, but this can be intrusive and time-consuming for those involved. In this protocol, participants undergo at-home sleep monitoring with multiple devices: 1) a single-channel EEG device; 2) a home sleep test for sleep-disordered breathing and periodic limb movements; 3) actigraphy; and 4) sleep logs. A major challenge of this study is obtaining high-quality sleep monitoring data on the first attempt in order to minimize participant burden. This protocol describes the implementation of educational manuals with step-by-step instructions and photos. The goal is to improve the quality of home sleep testing.

Here, we present a protocol to improve the quality of data from home sleep testing by providing a method to enhance instructions through a structured participant visit. This protocol includes the implementation of a step-by-step educational manual with photos to ensure proper placement of equipment.

The gold standard for sleep monitoring is attended in-lab polysomnography; however, this method may be cost-prohibitive and inconvenient for patients and ...

Quantitative Mapping of Specific Ventilation in the Human Lung using Proton Magnetic Resonance Imaging and Oxygen as a Contrast Agent

Specific ventilation imaging (SVI) is a functional magnetic resonance imaging technique capable of quantifying specific ventilation &#8213; the ratio of the fresh gas entering a lung region divided by the region&#8217;s end-expiratory volume &#8213; in the human lung, using only inhaled oxygen as a contrast agent. Regional quantification of specific ventilation has the potential to help identify areas of pathologic lung function. Oxygen in solution in tissue shortens the tissue&#8217;s longitudinal relaxation time (T1), and thus a change in tissue oxygenation can be detected as a change in T1-weighted signal with an inversion recovery acquired image. Following an abrupt change between two concentrations of inspired oxygen, the rate at which lung tissue within a voxel equilibrates to a new steady-state reflects the rate at which resident gas is being replaced by inhaled gas. This rate is determined by specific ventilation. To elicit this sudden change in oxygenation, subjects alternately breathe 20-breath blocks of air (21% oxygen) and 100% oxygen while in the MRI scanner. A stepwise change in inspired oxygen fraction is achieved through use of a custom three-dimensional (3D)-printed flow bypass system with a manual switch during a short end-expiratory breath hold. To detect the corresponding change in T1, a global inversion pulse followed by a single shot fast spin echo sequence was used to acquire two-dimensional T1-weighted images in a 1.5&#160;T MRI scanner, using an eight-element torso coil. Both single slice and multi-slice imaging are possible, with slightly different imaging parameters. Quantification of specific ventilation is achieved by correlating the time-course of signal intensity for each lung voxel with a library of simulated responses to the air/oxygen stimulus. SVI estimations of specific ventilation heterogeneity have been validated against multiple breath washout and proved to accurately determine the heterogeneity of the specific ventilation distribution.

Specific ventilation imaging is a functional magnetic resonance imaging technique that allows for quantification of regional specific ventilation in the human lung, using inhaled oxygen as a contrast agent. Here, we present a protocol to collect and analyze specific ventilation imaging data.

Specific ventilation imaging (SVI) is a functional magnetic resonance imaging technique capable of quantifying specific ventilation &#8213; the ratio of ...

Synthesis and Characterization of Multi-Modal Phase-Change Porphyrin Droplets

Phase-change droplets are a class of ultrasound contrast agents that can convert into echogenic microbubbles in situ with the application of sufficient acoustic energy. Droplets are smaller and more stable than their microbubble counterparts. However, traditional ultrasound contrast agents are not trackable beyond acoustic feedback measurements, which makes quantifying contrast agent bio-distribution or accumulation ex vivo difficult. Researchers may have to rely on fluorescent or optically absorbent companion diagnostic particles to infer bio-distribution. The purpose of this protocol is to detail steps for creating multi-modal phase-change porphyrin droplets using a condensation method. Porphyrins are fluorescent molecules with distinct absorbance bands that can be conjugated onto lipids and incorporated into droplets to extend droplet versatility, enabling more robust bio-distribution while retaining acoustic properties. Seven formulations with varying porphyrin-lipid and base lipid contents were made to investigate microbubble and droplet size distributions. Characterizations suited to porphyrin-containing structures are also described in the protocol to demonstrate their analytic versatility in-solution. Sizing showed that the post-condensed mean diameters were 1.72 to 2.38 times smaller than precursor populations. Absorbance characterization showed intact assemblies had a Q-band peak of 700 nm while disrupted samples had an absorbance peak at 671 nm. Fluorescence characterization showed intact 30% porphyrin-lipid assemblies were fluorescently quenched (&gt;97%), with fluorescence recovery achieved upon disruption. Acoustic vaporization showed that porphyrin droplets were non-echogenic at lower pressures and could be converted into echogenic microbubbles with sufficient pressures. These characterizations show the potential for porphyrin droplets to eliminate the need for absorbance or fluorescence-based companion diagnostic strategies to quantify ultrasound contrast agent bio-distribution for delivery or therapeutic applications in vivo or ex vivo.

In this protocol, methods for synthesizing and characterizing multi-modal phase-change porphyrin droplets are outlined.

Phase-change droplets are a class of ultrasound contrast agents that can convert into echogenic microbubbles in situ with the application of sufficient ...

Assessing Lung Function with Hyperpolarized Xenon-129 MRI

Quantitative Measure of Lung Structure and Function Obtained from Hyperpolarized Xenon Spectroscopy

Hyperpolarized Xenon-129 (HXe) magnetic resonance imaging (MRI) provides tools for obtaining 2- or 3-dimensional maps of lung ventilation patterns, gas diffusion, Xenon uptake by lung parenchyma, and other lung function metrics. However, by trading spatial for temporal resolution, it also enables tracing of pulmonary Xenon gas exchange on a ms timescale. This article describes one such technique, chemical shift saturation recovery (CSSR) MR spectroscopy. It illustrates how it can be used to assess capillary blood volume, septal wall thickness, and the surface-to-volume ratio in the alveoli. The flip angle of the applied radiofrequency pulses (RF) was carefully calibrated. Single-dose breath-hold and multi-dose free-breathing protocols were employed for administering the gas to the subject. Once the inhaled Xenon gas reached the alveoli, a series of 90&#176; RF pulses was applied to ensure maximum saturation of the accumulated Xenon magnetization in the lung parenchyma. Following a variable delay time, spectra were acquired to quantify the regrowth of the Xenon signal due to gas exchange between the alveolar gas volume and the tissue compartments of the lung. These spectra were then analyzed by fitting complex pseudo-Voigt functions to the three dominant peaks. Finally, the delay time-dependent peak amplitudes were fitted to a one-dimensional analytical gas-exchange model to extract physiological parameters.

Author Spotlight: Advancing Lung Disease Research with Free-Breathing Hyperpolarized Xenon-129 MRI

The manuscript presents a detailed protocol for using hyperpolarized Xenon-129 chemical shift saturation recovery (CSSR) to trace pulmonary gas exchange, assess the apparent alveolar septal wall thickness, and measure the surface-to-volume ratio. The method has the potential to diagnose and monitor lung diseases.

Hyperpolarized Xenon-129 (HXe) magnetic resonance imaging (MRI) provides tools for obtaining 2- or 3-dimensional maps of lung ventilation patterns, gas ...

Multi-modal Pulmonary Imaging: Using Complementary Information from CT and Hyperpolarized ¹²⁹Xe MRI to Evaluate Lung Structure-Function

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