Automated measurement of heterogeneity in CT images of healthy and diseased rat lungs using variogram analysis of an octree decomposition

The textures of sarcoidosis: quantifying lung disease through variograms

Objective

Sarcoidosis is a granulomatous disease affecting the lungs in over 90% of patients. Qualitative assessment of chest CT by radiologists is standard clinical practice and reliable quantification of disease from CT would support ongoing efforts to identify sarcoidosis phenotypes. Standard imaging feature engineering techniques such as radiomics suffer from extreme sensitivity to image acquisition and processing, potentially impeding generalizability of research to clinical populations. In this work, we instead investigate approaches to engineering variogram-based features with the intent to identify a robust, generalizable pipeline for image quantification in the study of sarcoidosis.

Approach

For a cohort of more than 300 individuals with sarcoidosis, we investigated 24 feature engineering pipelines differing by decisions for image registration to a template lung, empirical and model variogram estimation methods, and feature harmonization for CT scanner model, and subsequently 48 sets of phenotypes produced through unsupervised clustering. We then assessed sensitivity of engineered features, phenotypes produced through unsupervised clustering, and sarcoidosis disease signal strength to pipeline.

Main results

We found that variogram features had low to mild association with scanner model and associations were reduced by image registration. For each feature type, features were also typically robust to all pipeline decisions except image registration. Strength of disease signal as measured by association with pulmonary function testing and some radiologist visual assessments was strong (optimistic AUC ≈ 0.9, p ≪ 0.0001 in models for architectural distortion, conglomerate mass, fibrotic abnormality, and traction bronchiectasis) and fairly consistent across engineering approaches regardless of registration and harmonization for CT scanner.

Significance

Variogram-based features appear to be a suitable approach to image quantification in support of generalizable research in pulmonary sarcoidosis.

Human fetal whole-body postmortem microfocus computed tomographic imaging

Perinatal autopsy is the standard method for investigating fetal death; however, it requires dissection of the fetus. Human fetal microfocus computed tomography (micro-CT) provides a generally more acceptable and less invasive imaging alternative for bereaved parents to determine the cause of early pregnancy loss compared with conventional autopsy techniques. In this protocol, we describe the four main stages required to image fetuses using micro-CT. Preparation of the fetus includes staining with the contrast agent potassium triiodide and takes 3-19 d, depending on the size of the fetus and the time taken to obtain consent for the procedure. Setup for imaging requires appropriate positioning of the fetus and takes 1 h. The actual imaging takes, on average, 2 h 40 min and involves initial test scans followed by high-definition diagnostic scans. Postimaging, 3 d are required to postprocess the fetus, including removal of the stain, and also to undertake artifact recognition and data transfer. This procedure produces high-resolution isotropic datasets, allowing for radio-pathological interpretations to be made and long-term digital archiving for re-review and data sharing, where required. The protocol can be undertaken following appropriate training, which includes both the use of micro-CT techniques and handling of postmortem tissue.

Investigation of optimal sample preparation conditions with potassium triiodide and optimal imaging settings for microfocus computed tomography of excised cat hearts

OBJECTIVE

To determine optimal sample preparation conditions with potassium triiodide (I₂KI) and optimal imaging settings for microfocus CT (micro-CT) of excised cat hearts.

SAMPLE

7 excised hearts (weight range, 10 to 17.6 g) obtained from healthy adult cats after euthanasia by IV injection of pentobarbital sodium.

PROCEDURES

Following excision, the hearts were preserved in 10% formaldehyde solution. Six hearts were immersed in 1.25% I₂KI solution (n = 3) or 2.5% I₂KI solution (3) for a 12-day period. Micro-CT images were acquired at time 0 (prior to iodination) then approximately every 24 and 48 hours thereafter to determine optimal sample preparation conditions (ie, immersion time and concentration of I₂KI solution). Identified optimal conditions were then used to prepare the seventh heart for imaging; changes in voltage, current, exposure time, and gain on image quality were evaluated to determine optimal settings (ie, maximal signal-to-noise and contrast-to-noise ratios). Images were obtained at a voxel resolution of 30 μm. A detailed morphological assessment of the main cardiac structures of the seventh heart was then performed.

RESULTS

Immersion in 2.5% I₂KI solution for 48 hours was optimal for sample preparation. The optimal imaging conditions included a tube voltage of 100 kV, current of 150 μA, and exposure time of 354 milliseconds; scan duration was 12 minutes.

CONCLUSIONS AND CLINICAL RELEVANCE

Results provided an optimal micro-CT imaging protocol for excised cat hearts prepared with I₂KI solution that could serve as a basis for future studies of micro-CT for high resolution 3-D imaging of cat hearts.

T1 , T1 contrast, and Ernst-angle images of four rat-lung pathologies

PURPOSE

To initiate the archive of relaxation-weighted images that may help discriminate between pulmonary pathologies relevant to acute respiratory distress syndrome. MRI has the ability to distinguish pathologies by providing a variety of different contrast mechanisms. Lungs have historically been difficult to image with MRI but image quality is sufficient to begin cataloging the appearance of pathologies in T₁ - and T₂ -weighted images. This study documents T₁ and the use of T₁ contrast with four experimental rat lung pathologies.

METHODS

Inversion-recovery and spoiled steady state images were made at 1.89 T to measure T₁ and document contrast in rats with atelectasis, lipopolysaccharide-induced inflammation, ventilator-induced lung injury (VILI), and injury from saline lavage. Higher-resolution Ernst-angle images were made to see patterns of lung infiltrations.

RESULTS

T₁ -weighted images showed minimal contrast between pathologies, similar to T₁ -weighted images of other soft tissues. Images taken shortly after magnetization inversion and displayed with inverted contrast highlight lung pathologies. Ernst-angle images distinguish the effects of T₁ relaxation and spin density and display distinctive patterns. T₁ for pathologies were: atelectasis, 1.25 ± 0.046 s; inflammation from instillation of lipopolysaccharide, 1.24 ± 0.015 s; VILI, 1.55 ± 0.064 s (p = 0.0022 vs. normal lung); and injury from saline lavage, 1.90±0.080 s (p = 0.0022 vs. normal lung; p = 0.0079 vs. VILI). T₁ of normal lung and erector spinae muscle were 1.25 ± 0.028 s and 1.02 ± 0.027 s, respectively (p = 0.0022).

CONCLUSIONS

Traditional T₁ -weighting is subtle. However, images made with inverted magnetization and inverted contrast highlight the pathologies and Ernst-angle images aid in distinguishing pathologies.

CT-Based Local Distribution Metric Improves Characterization of COPD

Parametric response mapping (PRM) of paired CT lung images has been shown to improve the phenotyping of COPD by allowing for the visualization and quantification of non-emphysematous air trapping component, referred to as functional small airways disease (fSAD). Although promising, large variability in the standard method for analyzing PRMfSAD has been observed. We postulate that representing the 3D PRMfSAD data as a single scalar quantity (relative volume of PRMfSAD) oversimplifies the original 3D data, limiting its potential to detect the subtle progression of COPD as well as varying subtypes. In this study, we propose a new approach to analyze PRM. Based on topological techniques, we generate 3D maps of local topological features from 3D PRMfSAD classification maps. We found that the surface area of fSAD (SfSAD) was the most robust and significant independent indicator of clinically meaningful measures of COPD. We also confirmed by micro-CT of human lung specimens that structural differences are associated with unique SfSAD patterns, and demonstrated longitudinal feature alterations occurred with worsening pulmonary function independent of an increase in disease extent. These findings suggest that our technique captures additional COPD characteristics, which may provide important opportunities for improved diagnosis of COPD patients.

Magnetic resonance imaging provides sensitive in vivo assessment of experimental ventilator-induced lung injury

Animal models play a critical role in the study of acute respiratory distress syndrome (ARDS) and ventilator-induced lung injury (VILI). One limitation has been the lack of a suitable method for serial assessment of acute lung injury (ALI) in vivo. In this study, we demonstrate the sensitivity of magnetic resonance imaging (MRI) to assess ALI in real time in rat models of VILI. Sprague-Dawley rats were untreated or treated with intratracheal lipopolysaccharide or PBS. After 48 h, animals were mechanically ventilated for up to 15 h to induce VILI. Free induction decay (FID)-projection images were made hourly. Image data were collected continuously for 30 min and divided into 13 phases of the ventilatory cycle to make cinematic images. Interleaved measurements of respiratory mechanics were performed using a flexiVent ventilator. The degree of lung infiltration was quantified in serial images throughout the progression or resolution of VILI. MRI detected VILI significantly earlier (3.8 ± 1.6 h) than it was detected by altered lung mechanics (9.5 ± 3.9 h, P = 0.0156). Animals with VILI had a significant increase in the Index of Infiltration (P = 0.0027), and early regional lung infiltrates detected by MRI correlated with edema and inflammatory lung injury on histopathology. We were also able to visualize and quantify regression of VILI in real time upon institution of protective mechanical ventilation. Magnetic resonance lung imaging can be utilized to investigate mechanisms underlying the development and propagation of ALI, and to test the therapeutic effects of new treatments and ventilator strategies on the resolution of ALI.

Comparison of CT-derived ventilation maps with deposition patterns of inhaled microspheres in rats

PURPOSE

Computer models for inhalation toxicology and drug-aerosol delivery studies rely on ventilation pattern inputs for predictions of particle deposition and vapor uptake. However, changes in lung mechanics due to disease can impact airflow dynamics and model results. It has been demonstrated that non-invasive, in vivo, 4DCT imaging (3D imaging at multiple time points in the breathing cycle) can be used to map heterogeneities in ventilation patterns under healthy and disease conditions. The purpose of this study was to validate ventilation patterns measured from CT imaging by exposing the same rats to an aerosol of fluorescent microspheres (FMS) and examining particle deposition patterns using cryomicrotome imaging.

MATERIALS AND METHODS

Six male Sprague-Dawley rats were intratracheally instilled with elastase to a single lobe to induce a heterogeneous disease. After four weeks, rats were imaged over the breathing cycle by CT then immediately exposed to an aerosol of ∼ 1 μm FMS for ∼ 5 minutes. After the exposure, the lungs were excised and prepared for cryomicrotome imaging, where a 3D image of FMS deposition was acquired using serial sectioning. Cryomicrotome images were spatially registered to match the live CT images to facilitate direct quantitative comparisons of FMS signal intensity with the CT-based ventilation maps.

RESULTS

Comparisons of fractional ventilation in contiguous, non-overlapping, 3D regions between CT-based ventilation maps and FMS images showed strong correlations in fractional ventilation (r = 0.888, p < 0.0001).

CONCLUSION

We conclude that ventilation maps derived from CT imaging are predictive of the 1 μm aerosol deposition used in ventilation-perfusion heterogeneity inhalation studies.