While pulmonary disorders remain the leading causes of global morbidity and mortality1, the last decade has seen dramatic improvements in patient outcomes. These improvements are driven in part by two factors. Firstly, Phase III clinical trials now prioritize changes in lung function as endpoints rather than mortality, accelerating drug trials2,3,4,5. Secondly, advancements in improved animal models have provided insights into disease mechanisms and aided therapy development6,7. Mouse models are often favored for translational research because they offer physiological parallels to humans, affordability, and rapid disease development. Genetic engineering has expanded the range and quality of available models, with the International Mouse Strain Resource now boasting over 32,000 mouse strains8, compared to only 4,218 rat strains (Rat Genome Database9). These models have opened new avenues for investigating mechanistic drivers and therapy responses for a range of lung diseases, including chronic obstructive pulmonary disease (COPD)10, cystic fibrosis (CF)11, pulmonary fibrosis12,13, pulmonary hypertension14,15, and asthma16.
Unfortunately, lung research involving mice is limited by the techniques available to quantify disease burden. Studies often rely on terminal procedures that 1) provide whole-lung information (biochemical assays) or localized information (histology) and 2) demand cross-sectional designs and large sample sizes. Thus, they capture neither spatial nor temporal disease dynamics. In contrast, non-invasive, three-dimensional imaging can assess structure, molecular processes, and function in the lungs over time.
Lung structure (e.g., airway abnormalities and interstitial fibrosis) can be visualized with ultra-short echo-time (UTE) MRI and microcomputed tomography (µCT) at high resolution. Functional and mechanistic information (e.g., ventilation, perfusion, tumor metabolism, and inflammatory processes) can be obtained with exogenous contrast agents (e.g., xenon-enhanced CT and oxygen-enhanced UTE) and ionizing nuclear medicine approaches (i.e., positron emission tomography [PET], and single-photon emission computed tomography [SPECT]). However, functional imaging is challenging due to the modest contrast-to-noise (particularly for oxygen-enhanced UTE at the high magnetic field strengths used for preclinical MRI, where T1 is lengthened) available without employing ionizing modalities with higher than normal levels of radiation. While imaging with these modalities is well tolerated in animal models using conventional doses, cumulative radiation may confound results in studies on immunology, inflammation, and lung cancer17. However, hyperpolarized (HP) xenon-129 (129Xe) magnetic resonance imaging (MRI) provides minimally invasive, non-irradiating, and highly sensitive structural and functional information. While this technique has been employed in preclinical research to characterize conditions including emphysema18,19, fibrosis20, lung cancer21, COPD22, and radiation-induced lung injury23 at single or multiple time points, it remains underutilized in the preclinical setting.
To enable routine, preclinical 129Xe MRI, several prerequisites are required, including institutional regulatory support, a hyperpolarization device, a 129Xe-tuned radiofrequency (RF) coil, and a multi-nuclear-capable scanner. Although advanced applications24,25,26,27,28,29,30,31,32,33 require vendor-specific pulse programming that is outside of the scope of this protocol, basic applications can be achieved with modest software modifications. Therefore, we focus on quality control, magnetization handling, data collection, and animal handling procedures — including mechanical ventilation — that are unique to preclinical 129Xe MRI (Figure 1).
To date, small animal 129Xe imaging has employed three MR-safe gas delivery approaches, each with advantages and disadvantages: free-breathing, piston-driven, and pressure-drop. Free-breathing allows spontaneous inhalation without risk of injury from intubation or tracheostomy but consumes significantly more HP gas and can introduce motion artifacts34,35. Commercial piston-driven devices are self-calibrating and easy to use out-of-the-box but may be prohibitively expensive36. The pressure-drop-based approach used here is well described in the literature, modular, customizable, and run by open-source code37,38,39,40. Furthermore, it is cost-effective, typically totaling less than $10k and a few weeks of dedicated build time. The pressure-drop ventilator delivers 129Xe from a dose bag within a pressurized cannister while monitoring the airway pressure of an intubated mouse.

Figure 1: Overview of the protocol to collect routine xenon-129 (129Xe) magnetic resonance imaging (MRI) in mice. (A) Steps for initial setup. (Note: scanner programming is unique to each vendor and not described in this protocol). (B) Steps to collect daily quality assurance (QA) and animal data. (C) Steps for successful experiment conclusion and data analysis. Please click here to view a larger version of this figure.
Here, we collect and analyze the three common classes of 129Xe MRI data: ventilation, diffusion-weighted imaging (alveolar-airspace size), and gas exchange. Ventilation images depict the distribution of inhaled 129Xe gas. Regions of the lungs with reduced airflow appear dark in HP gas images, and pathology is quantified by the volume of defective ventilation. In humans, the ventilation defect percentage (VDP) has shown strong repeatability41,42 and high sensitivity to lung obstruction in diseases like COPD43,44,45 and asthma46,47.
The restricted diffusion of the 129Xe atoms in the airspace can be measured via the apparent diffusion coefficient (ADC) and serves as a surrogate for air-space size. The ADC is calculated by acquiring a baseline image (b0) without diffusion weighting and one or more images acquired in the presence of bipolar gradient-induced diffusion weighting (bN). An elevated ADC reflects an increase in airspace size due to aging or emphysematous remodeling18,48. Further, using multiple b-value images (≥4) allows more detailed morphometric information (e.g., mean linear intercept) to be calculated49,50.
Gas exchange can be characterized due to 1) the solubility of 129Xe in the capillary membrane tissue, plasma, and RBCs (red blood cells) and 2) the >200 ppm downfield chemical shift of 129Xe when dissolved in these compartments. Both spectroscopic and imaging data provide insight into cardiopulmonary diseases (e.g., pulmonary hypertension and left heart failure51,52,53). While many species (humans, canines, and rats) display unique spectral peaks originating from each compartment, mice lack a unique RBC signal due to differences in hemoglobin-xenon binding site interactions. Instead, all dissolved components are combined into a single signal in mice54. However, it is possible to observe a distinct RBC resonance in transgenic mice expressing human hemoglobin, such as those used in models of sickle cell disease54. Overall, dissolved 129Xe spectroscopy and imaging provide unique insights into cardiopulmonary pathophysiology in mice55,56.
Before attempting this protocol, it is necessary to understand background information about the MRI scanner, mechanical ventilation, and mouse handling techniques required for mouse studies. Prior to initiating animal studies, all procedures must be approved by the local Institutional Animal Care and Use Committee (IACUC)57. Because the total magnetic moment available in the mouse lung is intrinsically low (i.e., tidal volume ~250 µL), voxel size must be 1000-fold smaller than in humans to achieve anatomically equivalent resolution. The murine breathing rate is also exceedingly rapid (>100 breaths/minute). As such, the single-breath-hold procedures typically used for human imaging are not feasible. Instead, only a few RF excitations can be applied within each breath, so 129Xe images must be encoded over tens to hundreds of breaths. Pulse programming may be required to permit external triggering of acquisitions and to properly loop slices, phase encodes, and/or diffusion-weighted images while balancing signal-to-noise ratio (SNR), resolution, and scan duration. Here, the ventilator outputs a transistor-transistor logic (TTL) pulse once per breath to trigger data acquisition (Figure 2).

Figure 2: Representative mechanical ventilation and data acquisition timing. (A) User-controlled ventilation can trigger data acquisition at end-inspiration, during the breath hold, or at end-expiration. (B) For this 3D radial ventilation sequence, the user defines the total number of projections acquired and the number of projections per breath. (C) For a slice-selective, 2D diffusion-weighted image, the user defines the order of slices, b-value images, and phase encodes. Please click here to view a larger version of this figure.
To enable reliable ventilation and 129Xe delivery, robust sedation and intubation procedures are required. For each study, the downstream effects of each anesthetic must be considered - including changes to minute ventilation, heart rate (HR), and blood pressure58,59,60,61,62,63,64,65,66. While a variety of sedatives have been used for preclinical HP gas MRI, we employ a mixture of ketamine, xylazine, and acepromazine, due to its availability, cost-effectiveness, reliability, and duration67,68. Once sedated, animals must be intubated for effective mechanical ventilation. Intubation of mice is difficult due to the small size of their anatomy, and thus, it is important to train thoroughly in this technique. We encourage investigators to review published video protocols69,70. Because most commercial intubation cannulas contain stainless steel, we introduce a technique to craft metal-free (i.e., MRI and HP-gas compatible), wedge-shaped cannulas that can be customized to match airway diameter to create an airtight seal with the mouse tracheal wall.
Because 129Xe images are collected over many breaths, ventilator settings are critical. Protective ventilation strategies must be carefully considered to prevent lung injury71,72,73,74. In particular, the use of low tidal volume (TV), moderate positive end-expiratory pressure (PEEP), and alveolar recruitment maneuvers (RMs) reduce the risk of ventilator-induced lung injury in human patients and animal models75,76,77,78,79,80,81. Here, we recommend a simple technique that is compatible with pressure-drop 129Xe mechanical ventilation that is protective and provides sufficient 129Xe image SNR. Specifically, we apply PEEP by adding a commercial PEEP valve to the exhale line of the ventilator. To perform RMs, the exhalation line must be closed so that the animal receives multiple inhalations without exhalation until a target pressure and duration have been reached.
Throughout, we provide general ventilation settings, but it is advised to review the literature to address specific study goals82,83. In addition to monitoring the peak inspiratory pressure during mechanical ventilation, it is important to monitor the animal's temperature, which can be done using standard mouse temperature monitoring methods. While not required for imaging, monitoring heart rate via electrocardiogram (ECG) can be advantageous; ECG can indicate if an animal is waking from sedation, overdosed, or distressed, allowing the researcher to intervene.
The protocol we describe is designed to collect 129Xe 3D radial ventilation data61, 2D GRE diffusion-weighted data76, and dynamic pulse-acquire spectroscopy gas exchange data. This protocol aims to bridge the gap between preclinical research in small animal models and the potential for 129Xe MRI to advance our understanding of pulmonary disorders.