Co-Clinical Imaging Metadata Information (CIMI) for Cancer Research to Promote Open Science, Standardization, and Reproducibility in Preclinical Imaging.

Preclinical imaging is a critical component in translational research with significant complexities in workflow and site differences in deployment. Importantly, the National Cancer Institute's (NCI) precision medicine initiative emphasizes the use of translational co-clinical oncology models to address the biological and molecular bases of cancer prevention and treatment. The use of oncology models, such as patient-derived tumor xenografts (PDX) and genetically engineered mouse models (GEMMs), has ushered in an era of co-clinical trials by which preclinical studies can inform clinical trials and protocols, thus bridging the translational divide in cancer research. Similarly, preclinical imaging fills a translational gap as an enabling technology for translational imaging research. Unlike clinical imaging, where equipment manufacturers strive to meet standards in practice at clinical sites, standards are neither fully developed nor implemented in preclinical imaging. This fundamentally limits the collection and reporting of metadata to qualify preclinical imaging studies, thereby hindering open science and impacting the reproducibility of co-clinical imaging research. To begin to address these issues, the NCI co-clinical imaging research program (CIRP) conducted a survey to identify metadata requirements for reproducible quantitative co-clinical imaging. The enclosed consensus-based report summarizes co-clinical imaging metadata information (CIMI) to support quantitative co-clinical imaging research with broad implications for capturing co-clinical data, enabling interoperability and data sharing, as well as potentially leading to updates to the preclinical Digital Imaging and Communications in Medicine (DICOM) standard.

Automated multimodal segmentation of acute ischemic stroke lesions on clinical MR images.

Magnetic resonance (MR) imaging (MRI) is commonly used to diagnose, assess and monitor stroke. Accurate and timely segmentation of stroke lesions provides the anatomico-structural information that can aid physicians in predicting prognosis, as well as in decision making and triaging for various rehabilitation strategies. To segment stroke lesions, MR protocols, including diffusion-weighted imaging (DWI) and T2-weighted fluid attenuated inversion recovery (FLAIR) are often utilized. These imaging sequences are usually acquired with different spatial resolutions due to time constraints. Within the same image, voxels may be anisotropic, with reduced resolution along slice direction for diffusion scans in particular. In this study, we evaluate the ability of 2D and 3D U-Net Convolutional Neural Network (CNN) architectures to segment ischemic stroke lesions using single contrast (DWI) and dual contrast images (T2w FLAIR and DWI). The predicted segmentations correlate with post-stroke motor outcome measured by the National Institutes of Health Stroke Scale (NIHSS) and Fugl-Meyer Upper Extremity (FM-UE) index based on the lesion loads overlapping the corticospinal tracts (CST), which is a neural substrate for motor movement and function. Although the four methods performed similarly, the 2D multimodal U-Net achieved the best results with a mean Dice of 0.737 (95% CI: 0.705, 0.769) and a relatively high correlation between the weighted lesion load and the NIHSS scores (both at baseline and at 90 days). A monotonically constrained quintic polynomial regression yielded R2 = 0.784 and 0.875 for weighted lesion load versus baseline and 90-Days NIHSS respectively, and better corrected Akaike information criterion (AICc) scores than those of the linear regression. In addition, using the quintic polynomial regression model to regress the weighted lesion load to the 90-Days FM-UE score results in an R2 of 0.570 with a better AICc score than that of the linear regression. Our results suggest that the multi-contrast information enhanced the accuracy of the segmentation and the prediction accuracy for upper extremity motor outcomes. Expanding the training dataset to include different types of stroke lesions and more data points will help add a temporal longitudinal aspect and increase the accuracy. Furthermore, adding patient-specific data may improve the inference about the relationship between imaging metrics and functional outcomes.

Photon Counting CT and Radiomic Analysis Enables Differentiation of Tumors Based on Lymphocyte Burden.

The purpose of this study was to investigate if radiomic analysis based on spectral micro-CT with nanoparticle contrast-enhancement can differentiate tumors based on lymphocyte burden. High mutational load transplant soft tissue sarcomas were initiated in Rag2+/- and Rag2-/- mice to model varying lymphocyte burden. Mice received radiation therapy (20 Gy) to the tumor-bearing hind limb and were injected with a liposomal iodinated contrast agent. Five days later, animals underwent conventional micro-CT imaging using an energy integrating detector (EID) and spectral micro-CT imaging using a photon-counting detector (PCD). Tumor volumes and iodine uptakes were measured. The radiomic features (RF) were grouped into feature-spaces corresponding to EID, PCD, and spectral decomposition images. The RFs were ranked to reduce redundancy and increase relevance based on TL burden. A stratified repeated cross validation strategy was used to assess separation using a logistic regression classifier. Tumor iodine concentration was the only significantly different conventional tumor metric between Rag2+/- (TLs present) and Rag2-/- (TL-deficient) tumors. The RFs further enabled differentiation between Rag2+/- and Rag2-/- tumors. The PCD-derived RFs provided the highest accuracy (0.68) followed by decomposition-derived RFs (0.60) and the EID-derived RFs (0.58). Such non-invasive approaches could aid in tumor stratification for cancer therapy studies.

Detection of Lung Nodules in Micro-CT Imaging Using Deep Learning.

We are developing imaging methods for a co-clinical trial investigating synergy between immunotherapy and radiotherapy. We perform longitudinal micro-computed tomography (micro-CT) of mice to detect lung metastasis after treatment. This work explores deep learning (DL) as a fast approach for automated lung nodule detection. We used data from control mice both with and without primary lung tumors. To augment the number of training sets, we have simulated data using real augmented tumors inserted into micro-CT scans. We employed a convolutional neural network (CNN), trained with four competing types of training data: (1) simulated only, (2) real only, (3) simulated and real, and (4) pretraining on simulated followed with real data. We evaluated our model performance using precision and recall curves, as well as receiver operating curves (ROC) and their area under the curve (AUC). The AUC appears to be almost identical (0.76-0.77) for all four cases. However, the combination of real and synthetic data was shown to improve precision by 8%. Smaller tumors have lower rates of detection than larger ones, with networks trained on real data showing better performance. Our work suggests that DL is a promising approach for fast and relatively accurate detection of lung tumors in mice.

Overcoming detector limitations of x-ray photon counting for preclinical microcomputed tomography.

Spectral computed tomography (CT) using photon counting detectors (PCDs) can provide accurate tissue composition measurements by utilizing the energy dependence of x-ray attenuation in different materials. PCDs are especially suited for K-edge imaging, revealing the spatial distribution of select imaging probes through quantitative material decomposition. We report on a prototype spectral micro-CT system with a CZT-based PCD (DxRay, Inc.) that has 16 × 16 pixels of 0.5 × 0.5 mm 2 , a thickness of 3 mm, and four energy thresholds. Due to the PCD's limited size ( 8 × 8 mm 2 ), our system uses a translate-rotate projection acquisition strategy to cover a field of view relevant for preclinical imaging ( ∼ 4.5 cm ). Projection corrections were implemented to minimize artifacts associated with dead pixels and projection stitching. A sophisticated iterative algorithm was used to reconstruct both phantom and ex vivo mouse data. To achieve preclinically relevant spatial resolution, we trained a convolutional neural network to perform pan-sharpening between low-resolution PCD data ( 247 - µ m voxels) and high-resolution energy-integrating detector data ( 82 - µ m voxels), recovering a high-resolution estimate of the spectral contrast suitable for material decomposition. Long-term, preclinical spectral CT systems such as ours could serve in the developing field of theranostics (therapy and diagnostics) for cancer research.

Photon-counting cine-cardiac CT in the mouse.

The maturation of photon-counting detector (PCD) technology promises to enhance routine CT imaging applications with high-fidelity spectral information. In this paper, we demonstrate the power of this synergy and our complementary reconstruction techniques, performing 4D, cardiac PCD-CT data acquisition and reconstruction in a mouse model of atherosclerosis, including calcified plaque. Specifically, in vivo cardiac micro-CT scans were performed in four ApoE knockout mice, following their development of calcified plaques. The scans were performed with a prototype PCD (DECTRIS, Ltd.) with 4 energy thresholds. Projections were sampled every 10 ms with a 10 ms exposure, allowing the reconstruction of 10 cardiac phases at each of 4 energies (40 total 3D volumes per mouse scan). Reconstruction was performed iteratively using the split Bregman method with constraints on spectral rank and spatio-temporal gradient sparsity. The reconstructed images represent the first in vivo, 4D PCD-CT data in a mouse model of atherosclerosis. Robust regularization during iterative reconstruction yields high-fidelity results: an 8-fold reduction in noise standard deviation for the highest energy threshold (relative to unregularized algebraic reconstruction), while absolute spectral bias measurements remain below 13 Hounsfield units across all energy thresholds and scans. Qualitatively, image domain material decomposition results show clear separation of iodinated contrast and soft tissue from calcified plaque in the in vivo data. Quantitatively, spatial, spectral, and temporal fidelity are verified through a water phantom scan and a realistic MOBY phantom simulation experiment: spatial resolution is robustly preserved by iterative reconstruction (10% MTF: 2.8-3.0 lp/mm), left-ventricle, cardiac functional metrics can be measured from iodine map segmentations with ~1% error, and small calcifications (615 µm) can be detected during slow moving phases of the cardiac cycle. Given these preliminary results, we believe that PCD technology will enhance dynamic CT imaging applications with high-fidelity spectral and material information.

Dual-wavelength reflectance spectroscopy of the superior vena cava: A method for placing central venous catheters at the cavoatrial junction.

There are a limited number of methods to guide and confirm the placement of a peripherally inserted central catheter (PICC) at the cavoatrial junction. The aim of this study was to design, test and validate a dual-wavelength, diode laser-based, single optical fiber instrument that would accurately confirm PICC tip location at the cavoatrial junction of an animal heart, in vivo. This was accomplished by inserting the optical fiber into a PICC and ratiometrically comparing simultaneous visible and near-infrared reflection intensities of venous and atrial tissues found near the cavoatrial junction. The system was successful in placing the PICC line tip within 5 mm of the cavoatrial junction.

Renal sympathetic denervation using MR-guided high-intensity focused ultrasound in a porcine model.

BACKGROUND: Initial catheter-based renal sympathetic denervation (RSD) studies demonstrated promising results in showing a significant reduction of blood pressure, while recent data were less successful. As an alternative approach, the objective of this study was to evaluate the feasibility of using magnetic resonance-guided high-intensity focused ultrasound (MRgHIFU) to perform RSD in a porcine model. METHODS: An intravascular fiber optic temperature probe was used to confirm energy delivery during MRgHIFU. This technique was evaluated both in a vascular phantom and in a normotensive pig model. Five animals underwent unilateral RSD using MRgHIFU, and both safety and efficacy were assessed. MRI was used to evaluate the acoustic window, target sonications, monitor the near-field treatment region using MR thermometry imaging, and assess the status of tissues post-procedure. An intravascular fiber optic temperature probe verified energy delivery. Animals were sacrificed 6 to 9 days post-treatment, and pathological analysis was performed. The norepinephrine present in the kidney medulla was assessed post-mortem. RESULTS: All animals tolerated the procedure well with no observed complications. The fiber optic temperature probe placed in the target renal artery confirmed energy delivery during MRgHIFU, measuring larger temperature rises when the MRgHIFU beam location was focused closer to the tip of the probe. Following ablation, a significant reduction (p = 0.04) of cross-sectional area of nerve bundles between the treated and untreated renal arteries was observed in all of the animals with treated nerves presenting increased cellular infiltrate and fibrosis. A reduction of norepinephrine (p = 0.14) in the kidney medulla tissue was also observed. There was no indication of tissue damage in arterial walls. CONCLUSIONS: Performing renal denervation non-invasively with MRgHIFU was shown to be both safe and effective as determined by norepinephrine levels in a porcine model. This approach may be a promising alternative to catheter-based strategies.

The impact of modified Hatha yoga on chronic low back pain: a pilot study.

PURPOSE: The purpose of this randomized pilot study was to evaluate a possible design for a 6-week modified hatha yoga protocol to study the effects on participants with chronic low back pain. PARTICIPANTS: Twenty-two participants (M = 4; F = 17), between the ages of 30 and 65, with chronic low back pain (CLBP) were randomized to either an immediate yoga based intervention, or to a control group with no treatment during the observation period but received later yoga training. METHODS: A specific CLBP yoga protocol designed and modified for this population by a certified yoga instructor was administered for one hour, twice a week for 6 weeks. Primary functional outcome measures included the forward reach (FR) and sit and reach (SR) tests. All participants completed Oswestry Disability Index (ODI) and Beck Depression Inventory (BDI) questionnaires. Guiding questions were used for qualitative data analysis to ascertain how yoga participants perceived the instructor, group dynamics, and the impact of yoga on their life. ANALYSIS: To account for drop outs, the data were divided into better or not categories, and analyzed using chi-square to examine differences between the groups. Qualitative data were analyzed through frequency of positive responses. RESULTS: Potentially important trends in the functional measurement scores showed improved balance and flexibility and decreased disability and depression for the yoga group but this pilot was not powered to reach statistical significance. Significant limitations included a high dropout rate in the control group and large baseline differences in the secondary measures. In addition, analysis of the qualitative data revealed the following frequency of responses (1) group intervention motivated the participants and (2) yoga fostered relaxation and new awareness/learning. CONCLUSION: A modified yoga-based intervention may benefit individuals with CLB, but a larger study is necessary to provide definitive evidence. Also, the impact on depression and disability could be considered as important outcomes for further study. Additional functional outcome measures should be explored. This pilot study supports the need for more research investigating the effect of yoga for this population.