Three dimensional imaging of paraffin embedded human lung tissue samples by micro-computed tomography

A high-throughput 3D X-ray histology facility for biomedical research and preclinical applications

Background

The University of Southampton, in collaboration with the University Hospital Southampton (UHS) NHS Foundation Trust and industrial partners, has been at the forefront of developing three-dimensional (3D) imaging workflows using X-ray microfocus computed tomography (μCT) -based technology. This article presents the outcomes of these endeavours and highlights the distinctive characteristics of a μCT facility tailored explicitly for 3D X-ray Histology, with a primary focus on applications in biomedical research and preclinical and clinical studies.

Methods

The UHS houses a unique 3D X-ray Histology (XRH) facility, offering a range of services to national and international clients. The facility employs specialised μCT equipment explicitly designed for histology applications, allowing whole-block XRH imaging of formalin-fixed and paraffin-embedded tissue specimens. It also enables correlative imaging by combining μCT imaging with other microscopy techniques, such as immunohistochemistry (IHC) and serial block-face scanning electron microscopy, as well as data visualisation, image quantification, and bespoke analysis.

Results

Over the past seven years, the XRH facility has successfully completed over 120 projects in collaboration with researchers from 60 affiliations, resulting in numerous published manuscripts and conference proceedings. The facility has streamlined the μCT imaging process, improving productivity and enabling efficient acquisition of 3D datasets.

Discussion & Conclusions

The 3D X-ray Histology (XRH) facility at UHS is a pioneering platform in the field of histology and biomedical imaging. To the best of our knowledge, it stands out as the world's first dedicated XRH facility, encompassing every aspect of the imaging process, from user support to data generation, analysis, training, archiving, and metadata generation. This article serves as a comprehensive guide for establishing similar XRH facilities, covering key aspects of facility setup and operation. Researchers and institutions interested in developing state-of-the-art histology and imaging facilities can utilise this resource to explore new frontiers in their research and discoveries.

Feasibility and safety of synchrotron-based X-ray phase contrast imaging as a technique complementary to histopathology analysis

X-ray phase contrast imaging (X-PCI) is a powerful technique for high-resolution, three-dimensional imaging of soft tissue samples in a non-destructive manner. In this technical report, we assess the quality of standard histopathological techniques performed on formalin-fixed, paraffin-embedded (FFPE) human tissue samples that have been irradiated with different doses of X-rays in the context of an X-PCI experiment. The data from this study demonstrate that routine histochemical and immunohistochemical staining quality as well as DNA and RNA analyses are not affected by previous X-PCI on human FFPE samples. From these data we conclude it is feasible and acceptable to perform X-PCI on FFPE human biopsies.

The Value of Micro-CT in the Diagnosis of Lung Carcinoma: A Radio-Histopathological Perspective

Micro-computed tomography (micro-CT) is a relatively new imaging modality and the three-dimensional (3D) images obtained via micro-CT allow researchers to collect both quantitative and qualitative information on various types of samples. Micro-CT could potentially be used to examine human diseases and several studies have been published on this topic in the last decade. In this study, the potential uses of micro-CT in understanding and evaluating lung carcinoma and the relevant studies conducted on lung and other tumors are summarized. Currently, the resolution of benchtop laboratory micro-CT units has not reached the levels that can be obtained with light microscopy, and it is not possible to detect the histopathological features (e.g., tumor type, adenocarcinoma pattern, spread through air spaces) required for lung cancer management. However, its ability to provide 3D images in any plane of section, without disturbing the integrity of the specimen, suggests that it can be used as an auxiliary technique, especially in surgical margin examination, the evaluation of tumor invasion in the entire specimen, and calculation of primary and metastatic tumor volume. Along with future developments in micro-CT technology, it can be expected that the image resolution will gradually improve, the examination time will decrease, and the relevant software will be more user friendly. As a result of these developments, micro-CT may enter pathology laboratories as an auxiliary method in the pathological evaluation of lung tumors. However, the safety, performance, and cost effectiveness of micro-CT in the areas of possible clinical application should be investigated. If micro-CT passes all these tests, it may lead to the convergence of radiology and pathology applications performed independently in separate units today, and the birth of a new type of diagnostician who has equal knowledge of the histological and radiological features of tumors.

A Single-Cell Atlas of Small Airway Disease in Chronic Obstructive Pulmonary Disease: A Cross-Sectional Study

Rationale: Emerging data demonstrate that the smallest conducting airways, terminal bronchioles, are the early site of tissue destruction in chronic obstructive pulmonary disease (COPD) and are reduced by as much as 41% by the time someone is diagnosed with mild (Global Initiative for Chronic Obstructive Lung Disease [GOLD] stage 1) COPD. Objectives: To develop a single-cell atlas that describes the structural, cellular, and extracellular matrix alterations underlying terminal bronchiole loss in COPD. Methods: This cross-sectional study of 262 lung samples derived from 34 ex-smokers with normal lung function (n = 10) or GOLD stage 1 (n = 10), stage 2 (n = 8), or stage 4 (n = 6) COPD was performed to assess the morphology, extracellular matrix, single-cell atlas, and genes associated with terminal bronchiole reduction using stereology, micro-computed tomography, nonlinear optical microscopy, imaging mass spectrometry, and transcriptomics. Measurements and Main Results: The lumen area of terminal bronchioles progressively narrows with COPD severity as a result of the loss of elastin fibers within alveolar attachments, which was observed before microscopic emphysematous tissue destruction in GOLD stage 1 and 2 COPD. The single-cell atlas of terminal bronchioles in COPD demonstrated M1-like macrophages and neutrophils located within alveolar attachments and associated with the pathobiology of elastin fiber loss, whereas adaptive immune cells (naive, CD4, and CD8 T cells, and B cells) are associated with terminal bronchiole wall remodeling. Terminal bronchiole pathology was associated with the upregulation of genes involved in innate and adaptive immune responses, the interferon response, and the degranulation of neutrophils. Conclusions: This comprehensive single-cell atlas highlights terminal bronchiole alveolar attachments as the initial site of tissue destruction in centrilobular emphysema and an attractive target for disease modification.

Volumetric Tissue Imaging of Surgical Tissue Specimens Using Micro-Computed Tomography: An Emerging Digital Pathology Modality for Nondestructive, Slide-Free Microscopy-Clinical Applications of Digital Pathology in 3 Dimensions

OBJECTIVES

Micro-computed tomography (micro-CT) is a novel, nondestructive, slide-free digital imaging modality that enables the acquisition of high-resolution, volumetric images of intact surgical tissue specimens. The aim of this systematic mapping review is to provide a comprehensive overview of the available literature on clinical applications of micro-CT tissue imaging and to assess its relevance and readiness for pathology practice.

METHODS

A computerized literature search was performed in the PubMed, Scopus, Web of Science, and CENTRAL databases. To gain insight into regulatory and financial considerations for performing and examining micro-CT imaging procedures in a clinical setting, additional searches were performed in medical device databases.

RESULTS

Our search identified 141 scientific articles published between 2000 and 2021 that described clinical applications of micro-CT tissue imaging. The number of relevant publications is progressively increasing, with the specialties of pulmonology, cardiology, otolaryngology, and oncology being most commonly concerned. The included studies were mostly performed in pathology departments. Current micro-CT devices have already been cleared for clinical use, and a Current Procedural Terminology (CPT) code exists for reimbursement of micro-CT imaging procedures.

CONCLUSIONS

Micro-CT tissue imaging enables accurate volumetric measurements and evaluations of entire surgical specimens at microscopic resolution across a wide range of clinical applications.

Aggrecan accumulates at sites of increased pulmonary arterial pressure in idiopathic pulmonary arterial hypertension

Expansion of extracellular matrix occurs in all stages of pulmonary angiopathy associated with pulmonary arterial hypertension (PAH). In systemic arteries, dysregulation and accumulation of the large chondroitin-sulfate proteoglycan aggrecan is associated with swelling and disruption of vessel wall homeostasis. Whether aggrecan is present in pulmonary arteries, and its potential roles in PAH, has not been thoroughly investigated. Here, lung tissue from 11 patients with idiopathic PAH was imaged using synchrotron radiation phase-contrast microcomputed tomography (TOMCAT beamline, Swiss Light Source). Immunohistochemistry for aggrecan core protein in subsequently sectioned lung tissue demonstrated accumulation in PAH compared with failed donor lung controls. RNAscope in situ hybridization indicated ACAN expression in vascular endothelium and smooth muscle cells. Based on qualitative histological analysis, aggrecan localizes to cellular, rather than fibrotic or collagenous, lesions. Interestingly, ADAMTS15, a potential aggrecanase, was upregulated in pulmonary arteries in PAH. Aligning traditional histological analysis with three-dimensional renderings of pulmonary arteries from synchrotron imaging identified aggrecan in lumen-reducing lesions containing loose, cell-rich connective tissue, at sites of intrapulmonary bronchopulmonary shunting, and at sites of presumed elevated pulmonary blood pressure. Our findings suggest that ACAN expression may be an early response to injury in pulmonary angiopathy and supports recent work showing that dysregulation of aggrecan turnover is a hallmark of arterial adaptations to altered hemodynamics. Whether cause or effect, aggrecan and aggrecanase regulation in PAH are potential therapeutic targets.

A high-resolution 3D atlas of the spectrum of tuberculous and COVID-19 lung lesions

Our current understanding of the spectrum of TB and COVID-19 lesions in the human lung is limited by a reliance on low-resolution imaging platforms that cannot provide accurate 3D representations of lesion types within the context of the whole lung. To characterize TB and COVID-19 lesions in 3D, we applied micro/nanocomputed tomography to surgically resected, postmortem, and paraffin-embedded human lung tissue. We define a spectrum of TB pathologies, including cavitary lesions, calcium deposits outside and inside necrotic granulomas and mycetomas, and vascular rearrangement. We identified an unusual spatial arrangement of vasculature within an entire COVID-19 lobe, and 3D segmentation of blood vessels revealed microangiopathy associated with hemorrhage. Notably, segmentation of pathological anomalies reveals hidden pathological structures that might otherwise be disregarded, demonstrating a powerful method to visualize pathologies in 3D in TB lung tissue and whole COVID-19 lobes. These findings provide unexpected new insight into the spatial organization of the spectrum of TB and COVID-19 lesions within the framework of the entire lung.

Assessment of Deviations of Implants Installed with Prototyped Surgical Guide and Conventional Guide: In Vitro Study

OBJECTIVE

 The study aimed to assess the angular and linear deviations of implants installed in mannequins aided by surgical guides produced with the techniques of dual tomography (DT), model-based tomography (MT), and nonprototyped guide.

MATERIALS AND METHODS

 Implants were installed in mannequins of a partially edentulous maxilla and divided into three groups: Group C (n = 20), implants installed using the conventional technique with flap opening and conventional guide; Group DT (n = 20), implants installed using guided surgery with the dual tomography technique; and Group MT (n = 20), implants installed using the model-based tomography technique. After implant installation, the mannequin was subjected to a computed tomography (CT) to measure the linear and angular deviations of implant positioning relative to the initial planning on both sides.

RESULTS

 There was a higher mean angular deviation in group C (4.61 ± 1.21, p ≤ 0.001) than in groups DT (2.13 ± 0.62) and MT (1.87 ± 0.94), which were statistically similar between each other. Similarly, the linear deviations showed group C with the greatest discrepancy in relation to the other groups in the crown (2.17 ± 0.82, p = 0.007), central (2.2 ± 0.77, p = 0.004), and apical (2.34 ± 0.8, p = 0.001) regions.

CONCLUSION

 The techniques of DT and MT presented smaller angular and linear deviations than the conventional technique with the nonprototyped guide. There was no difference between the two-guided surgery techniques.

An optimized workflow for microCT imaging of formalin‐fixed and paraffin‐embedded ( FFPE ) early equine embryos

Here, we describe a workflow for high‐detail microCT imaging of formalin‐fixed and paraffin‐embedded (FFPE) equine embryos recovered on Day 34 of pregnancy (E34), a period just before placenta formation. The presented imaging methods are suitable for large animals' embryos with intention to study morphological and developmental aspects, but more generally can be adopted for all kinds of FFPE tissue specimens. Microscopic 3D imaging techniques such as microCT are important tools for detecting and studying normal embryogenesis and developmental disorders. To date, microCT imaging of vertebrate embryos was mostly done on embryos that have been stained with an X‐ray dense contrast agent. Here, we describe an alternative imaging procedure that allows to visualize embryo morphology and organ development in unstained FFPE embryos. Two aspects are critical for high‐quality data acquisition: (i) a proper sample mounting leaving as little as possible paraffin around the sample and (ii) an image filtering pipeline that improves signal‐to‐noise ratio in these inherently low‐contrast data sets. The presented workflow allows overview imaging of the whole embryo proper and can be used for determination of organ volumes and development. Furthermore, we show that high‐resolution interior tomographies can provide virtual histology information from selected regions of interest. In addition, we demonstrate that microCT scanned embryos remain intact during the scanning procedure allowing for a subsequent investigation by routine histology and/or immunohistochemistry. This makes the presented workflow applicable also to archival paraffin‐embedded material.

Nondestructive cellular-level 3D observation of mouse kidney using laboratory-based X-ray microscopy with paraffin-mediated contrast enhancement

For three-dimensional observation of unstained bio-specimens using X-ray microscopy with computed tomography (CT), one main problem has been low contrast in X-ray absorption. Here we introduce paraffin-mediated contrast enhancement to visualize biopsy samples of mouse kidney using a laboratory-based X-tray microscope. Unlike conventional heavy-atom staining, paraffin-mediated contrast enhancement uses solid paraffin as a negative contrast medium to replace water in the sample. The medium replacement from water to paraffin effectively lowers the absorption of low-energy X-rays by the medium, which eventually enhances the absorption contrast between the medium and tissue. In this work, paraffin-mediated contrast enhancement with 8 keV laboratory X-rays was used to visualize cylindrical renal biopsies with diameters of about 0.5 mm. As a result, reconstructed CT images from 19.4 h of data collection achieved cellular-level resolutions in all directions, which provided 3D structures of renal corpuscles from a normal mouse and from a disease model mouse. These two structures with and without disease allowed a volumetric analysis showing substantial volume differences in glomerular subregions. Notably, this nondestructive method presents CT opacities reflecting elemental composition and density of unstained tissues, thereby allowing more unbiased interpretation on their biological structures.

Patch-based artifact reduction for three-dimensional volume projection data of sparse-view micro-computed tomography

Micro-computed tomography (micro-CT) enables the non-destructive acquisition of three-dimensional (3D) morphological structures at the micrometer scale. Although it is expected to be used in pathology and histology to analyze the 3D microstructure of tissues, micro-CT imaging of tissue specimens requires a long scan time. A high-speed imaging method, sparse-view CT, can reduce the total scan time and radiation dose; however, it causes severe streak artifacts on tomographic images reconstructed with analytical algorithms due to insufficient sampling. In this paper, we propose an artifact reduction method for 3D volume projection data from sparse-view micro-CT. Specifically, we developed a patch-based lightweight fully convolutional network to estimate full-view 3D volume projection data from sparse-view 3D volume projection data. We evaluated the effectiveness of the proposed method using physically acquired datasets. The qualitative and quantitative results showed that the proposed method achieved high estimation accuracy and suppressed streak artifacts in the reconstructed images. In addition, we confirmed that the proposed method requires both short training and prediction times. Our study demonstrates that the proposed method has great potential for artifact reduction for 3D volume projection data under sparse-view conditions.

Origins of and lessons from quantitative functional X-ray computed tomography of the lung

Functional CT of the lung has emerged from quantitative CT (qCT). Structural details extracted at multiple lung volumes offer indices of function. Additionally, single volumetric images, if acquired at standardized lung volumes and body posture, can be used to model function by employing such engineering techniques as computational fluid dynamics. With the emergence of multispectral CT imaging including dual energy from energy integrating CT scanners and multienergy binning using the newly released photon counting CT technology, function is tagged via use of contrast agents. Lung disease phenotypes have previously been lumped together by the limitations of spirometry and plethysmography. QCT and its functional embodiment have been imbedded into studies seeking to characterize chronic obstructive pulmonary disease, severe asthma, interstitial lung disease and more. Reductions in radiation dose by an order of magnitude or more have been achieved. At the same time, we have seen significant increases in spatial and density resolution along with methodologic validations of extracted metrics. Together, these have allowed attention to turn towards more mild forms of disease and younger populations. In early applications, clinical CT offered anatomic details of the lung. Functional CT offers regional measures of lung mechanics, the assessment of functional small airways disease, as well as regional ventilation-perfusion matching (V/Q) and more. This paper will focus on the use of quantitative/functional CT for the non-invasive exploration of dynamic three-dimensional functioning of the breathing lung and beating heart within the unique negative pressure intrathoracic environment of the closed chest.

HREM, RNAseq and Cell Cycle Analyses Reveal the Role of the G2/M-Regulatory Protein, WEE1, on the Survivability of Chicken Embryos during Diapause

Avian blastoderm can enter into diapause when kept at low temperatures and successfully resume development (SRD) when re-incubated in body temperature. These abilities, which are largely affected by the temperature and duration of the diapause, are poorly understood at the cellular and molecular level. To determine how temperature affects embryonic morphology during diapause, high-resolution episcopic microscopy (HREM) analysis was utilized. While blastoderms diapausing at 12 °C for 28 days presented typical cytoarchitecture, similar to non-diapaused embryos, at 18 °C, much thicker blastoderms with higher cell number were observed. RNAseq was conducted to discover the genes underlying these phenotypes, revealing differentially expressed cell cycle regulatory genes. Among them, WEE1, a negative regulator of G2/M transition, was highly expressed at 12 °C compared to 18 °C. This finding suggested that cells at 12 °C are arrested at the G2/M phase, as supported by bromodeoxyuridine incorporation (BrdU) assay and phospho-histone H3 (pH 3) immunostaining. Inhibition of WEE1 during diapause at 12 °C resulted in cell cycle progression beyond the G2/M and augmented tissue volume, resembling the morphology of 18 °C-diapaused embryos. These findings suggest that diapause at low temperatures leads to WEE1 upregulation, which arrests the cell cycle at the G2/M phase, promoting the perseverance of embryonic cytoarchitecture and future SRD. In contrast, WEE1 is not upregulated during diapause at higher temperature, leading to continuous proliferation and maladaptive morphology associated with poor survivability. Combining HREM-based analysis with RNAseq and molecular manipulations, we present a novel mechanism that regulates the ability of diapaused avian embryos to maintain their cytoarchitecture via cell cycle arrest, which enables their SRD.

Micro-computed tomography: A novel diagnostic technique for the evaluation of gastrointestinal specimens

Micro-computed tomography (micro-CT) is a non-destructive modality that can be used to obtain high-resolution three-dimensional (3 D) images of the whole sample tissue; the usefulness of micro-CT has been reported for evaluation of breast cancer and lung cancer. However, this novel diagnostic technique has never been used for evaluating endoscopically resected gastrointestinal specimens. In the present study, we scanned 13 formalin-fixed paraffin-embedded (FFPE) tissue blocks of a normal human colon and gastric tissue samples using micro-CT. The evaluation comprised a comparison of the acquired whole block images with the images of the corresponding cross-sectional slice of the hematoxylin and eosin-stained slide. Micro-CT was able to produce images of the whole sample and clearly depict tissues such as glandular structures, muscularis mucosae, and blood vessels in the FFPE tissue blocks of normal gastrointestinal samples. Furthermore, the 3 D reconstructed could be used to create a cross-sectional image and reflected the surface structure of samples obtained from any site. Micro-CT has the potential to become a highly promising pathological diagnostic assistance tool for endoscopically resected gastrointestinal specimens in combination with conventional microscopic examination.

A localization-independent approach for invisible and impalpable ground-glass opacity nodules detection in an in vitro lung specimen: two case reports

A growing number of ground-glass opacity (GGO) nodules are screened out in lungs. Small GGOs are frequently neither visible nor palpable, thus undetectable during operation. Various nodule localization techniques have been developed to facilitate the intraoperative detection of GGO nodules; however, general localization techniques are infeasible or inappropriate in some cases. The detection of small GGO is a great challenge, even within a surgical specimen in the absence of preoperative localization. A localization-independent approach for GGO detection is urgently needed. Herein, we report two cases with invisible and impalpable small GGO which were not appropriate for preoperative localization. The lesions were anatomically resected under the guidance of three-dimensional (3D) reconstruction and got an adequate margin distance. A vessel (artery, vein, or bronchus) which had advanced into or immediately adjacent to the nodule was assigned as a reference vessel. By dissecting and tracing the reference vessel from proximal to distal, the GGO lesions were successfully detected in the surgical specimens, to the eventual obtainment of an accurate pathological diagnosis. Via the two case reports, we introduced an easily handled approach, namely dissecting and tracing a reference vessel, for GGO detection. The novel approach was first described. Combined with precise anatomical segmentectomy guided by 3D reconstruction, it provides an alternative scheme for GGO resection with no need for preoperative localization.

Volumetric Imaging of Lung Tissue at Micrometer Resolution: Clinical Applications of Micro-CT for the Diagnosis of Pulmonary Diseases

Micro-computed tomography (micro-CT) is a promising novel medical imaging modality that allows for non-destructive volumetric imaging of surgical tissue specimens at high spatial resolution. The aim of this study is to provide a comprehensive assessment of the clinical applications of micro-CT for the tissue-based diagnosis of lung diseases. This scoping review was conducted in accordance with the PRISMA Extension for Scoping Reviews, aiming to include every clinical study reporting on micro-CT imaging of human lung tissues. A literature search yielded 570 candidate articles, out of which 37 were finally included in the review. Of the selected studies, 9 studies explored via micro-CT imaging the morphology and anatomy of normal human lung tissue; 21 studies investigated microanatomic pulmonary alterations due to obstructive or restrictive lung diseases, such as chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, and cystic fibrosis; and 7 studies examined the utility of micro-CT imaging in assessing lung cancer lesions (n = 4) or in transplantation-related pulmonary alterations (n = 3). The selected studies reported that micro-CT could successfully detect several lung diseases providing three-dimensional images of greater detail and resolution than routine optical slide microscopy, and could additionally provide valuable volumetric insight in both restrictive and obstructive lung diseases. In conclusion, micro-CT-based volumetric measurements and qualitative evaluations of pulmonary tissue structures can be utilized for the clinical management of a variety of lung diseases. With micro-CT devices becoming more accessible, the technology has the potential to establish itself as a core diagnostic imaging modality in pathology and to enable integrated histopathologic and radiologic assessment of lung cancer and other lung diseases.

Immunofluorescence-guided segmentation of three-dimensional features in micro-computed tomography datasets of human lung tissue

Micro-computed tomography (µCT) provides non-destructive three-dimensional (3D) imaging of soft tissue microstructures. Specific features in µCT images can be identified using correlated two-dimensional (2D) histology images allowing manual segmentation. However, this is very time-consuming and requires specialist knowledge of the tissue and imaging modalities involved. Using a custom-designed µCT system optimized for imaging unstained formalin-fixed paraffin-embedded soft tissues, we imaged human lung tissue at isotropic voxel sizes less than 10 µm. Tissue sections were stained with haematoxylin and eosin or cytokeratin 18 in columnar airway epithelial cells using immunofluorescence (IF), as an exemplar of this workflow. Novel utilization of tissue autofluorescence allowed automatic alignment of 2D microscopy images to the 3D µCT data using scripted co-registration and automated image warping algorithms. Warped IF images, which were accurately aligned with the µCT datasets, allowed 3D segmentation of immunoreactive tissue microstructures in the human lung. Blood vessels were segmented semi-automatically using the co-registered µCT datasets. Correlating 2D IF and 3D µCT data enables accurate identification, localization and segmentation of features in fixed soft lung tissue. Our novel correlative imaging workflow provides faster and more automated 3D segmentation of µCT datasets. This is applicable to the huge range of formalin-fixed paraffin-embedded tissues held in biobanks and archives.

Recent advances in airway imaging using micro-computed tomography and computed tomography for chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a complex lung disease characterized by a combination of airway disease and emphysema. Emphysema is classified as centrilobular emphysema (CLE), paraseptal emphysema (PSE), or panlobular emphysema (PLE), and airway disease extends from the respiratory, terminal, and preterminal bronchioles to the central segmental airways. Although clinical computed tomography (CT) cannot be used to visualize the small airways, micro-CT has shown that terminal bronchiole disease is more severe in CLE than in PSE and PLE, and micro-CT findings suggest that the loss and luminal narrowing of terminal bronchioles is an early pathological change in CLE. Furthermore, the introduction of ultra-high-resolution CT has enabled direct evaluation of the proximal small (1 to 2-mm diameter) airways, and new CT analytical methods have enabled estimation of small airway disease and prediction of future COPD onset and lung function decline in smokers with and without COPD. This review discusses the literature on micro-CT and the technical advancements in clinical CT analysis for COPD. Hopefully, novel micro-CT findings will improve our understanding of the distinct pathogeneses of the emphysema subtypes to enable exploration of new therapeutic targets, and sophisticated CT imaging methods will be integrated into clinical practice to achieve more personalized management.

Usefulness of microfocus computed tomography in life science research: preliminary study using murine micro-hepatic tumor models

PURPOSE

Microfocus computed tomography (micro-CT) has not been widely used at high radiation intensity (industrial micro-CT) in life science fields. In this preliminary study, we investigated its potential value in the detection of micro-hepatic tumors in a mouse model.

METHODS

The liver with micro-hepatic tumors was surgically resected en-bloc from mice, and examined with industrial micro-CT and lower intensity micro-CT (small animal micro-CT). The number of hepatic tumors was manually counted on serial images. Then, the accuracy of each technique was determined by preparing matching liver sections and comparing the number of tumors identified in a conventional pathological examination.

RESULTS

The number of hepatic tumors evaluated with industrial micro-CT showed high concordance with the results of the pathological examinations (intraclass correlation coefficient [ICC]: 0.984; 95% confidence interval [CI] 0.959-0.994). On the other hand, the number of hepatic tumors evaluated with the small animal micro-CT showed low concordance with the number identified in the pathological examinations (ICC: 0.533; 95% CI 0.181-0.815).

CONCLUSION

Industrial micro-CT improved the detection of small structures in resected specimens, and might be a promising solution for life science research.

A quality optimization approach to image Achilles tendon microstructure by phase-contrast enhanced synchrotron micro-tomography

Achilles tendons are mechanosensitive, and their complex hierarchical structure is in part the result of the mechanical stimulation conveyed by the muscles. To fully understand how their microstructure responds to mechanical loading a non-invasive approach for 3D high resolution imaging suitable for soft tissue is required. Here we propose a protocol that can capture the complex 3D organization of the Achilles tendon microstructure, using phase-contrast enhanced synchrotron micro-tomography (SR-PhC-μCT). We investigate the effects that sample preparation and imaging conditions have on the resulting image quality, by considering four types of sample preparations and two imaging setups (sub-micrometric and micrometric final pixel sizes). The image quality is assessed using four quantitative parameters. The results show that for studying tendon collagen fibers, conventional invasive sample preparations such as fixation and embedding are not necessary or advantageous. Instead, fresh frozen samples result in high-quality images that capture the complex 3D organization of tendon fibers in conditions as close as possible to natural. The comprehensive nature of this innovative study by SR-PhC-μCT breaks ground for future studies of soft complex biological tissue in 3D with high resolution in close to natural conditions, which could be further used for in situ characterization of how soft tissue responds to mechanical stimuli on a microscopic level.

Complication and lung function impairment prediction using perfusion and computed tomography air trapping (CLIPPCAIR): protocol for the development and validation of a novel multivariable model for the prediction of post-resection lung function

Background

Recent advancements in computed tomography (CT) scanning and post processing have provided new means of assessing factors affecting respiratory function. For lung cancer patients requiring resection, and especially those with respiratory comorbidities such as chronic obstructive pulmonary disease (COPD), the ability to predict post-operative lung function is a crucial step in the lung cancer operability assessment. The primary objective of the CLIPPCAIR study is to use novel CT data to develop and validate an algorithm for the prediction of lung function remaining after pneumectomy/lobectomy.

Methods

Two sequential cohorts of non-small cell lung cancer patients requiring a pre-resection CT scan will be recruited at the Montpellier University Hospital, France: a test population (N=60) on which predictive models will be developed, and a further model validation population (N=100). Enrolment will occur during routine pre-surgical consults and follow-up visits will occur 1 and 6 months after pneumectomy/lobectomy. The primary outcome to be predicted is forced expiratory volume in 1 second (FEV1) six months after lung resection. The baseline CT variables that will be used to develop the primary multivariable regression model are: expiratory to inspiratory ratios of mean lung density (MLD_e/i for the total lung and resected volume), the percentage of voxels attenuating at less than ‒950 HU (PVOX_‒950 for the total lung and resected volume) and the ratio of iodine concentrations for the resected volume over that of the total lung. The correlation between predicted and real values will be compared to (and is expected to improve upon) that of previously published methods. Secondary analyses will include the prediction of transfer factor for carbon monoxide (TLCO) and complications in a similar fashion. The option to explore further variables as predictors of post-resection lung function or complications is kept open.

Discussion

Current methods for estimating post-resection lung function are imperfect and can add assessments (such as scintigraphy) to the pre-surgical workup. By using CT imaging data in a novel fashion, the results of the CLIPPCAIR study may not only improve such estimates, it may also simplify patient pathways.

Trial registration

Clinicaltrials.gov (NCT03885765).

Micro-CT processing's effects on microscopic appearance of human fetal cardiac samples

Higher resolution than common computed tomography has been reached through Micro-Computed Tomography (micro-CT) on small samples. Emerging forensic applications of micro-CT are the study of fetal/infant organs and whole fetuses, and their two/three-dimension reconstruction; it allows: to facilitate pathologists' role in the identification of causes of fetal stillbirth and of infant death; to create digital two and/or three-dimension representations of fetal/infant organs and whole fetuses which can be easily discussed in civil and/or penal courts. Micro-CT reconstructs cardiac anatomy of animal and human sample. There are no studies that are specifically aimed to evaluate possible effects of micro-CT processing on cardiac microscopic evaluation. This study analyzed microscopic effects of micro-CT processing on human-fetal-hearts. After processing with Lugol-solution or Microfil-MV-122-injection in coronary branches, fetal hearts underwent micro-CT scan. Then, hearts were microscopically analyzed using hematoxylin/eosin, trichrome, immunohistochemistry (IHC) for actin-protein, and IHC for desmin-intermediate-filament stains. In all cases staining was present in all fields. In all slides, disarranged myocardial proteins with increase of inter filaments and inter cellular spaces was reported. This manuscript allowed to observe post micro-CT appropriate staining and antigenic reactivity, and to identify cytoarchitecture modifications that could compromise slides' microscopic evaluation. It also highlighted a possible role of micro-CT determining this cytoarchitecture phenomenon.

Micro-CT Imaging of Pediatric Thyroglossal Duct Cysts: A Prospective Case Series

Objectives: To determine the feasibility of micro-CT as a high-resolution 3D imaging tool for thyroglossal duct cysts and to evaluate its role augmenting traditional histopathological examination of resected specimens. Methods: A single centre, prospective case series of consecutive children undergoing excision of a thyroglossal duct cyst was performed at a quaternary paediatric referral hospital in the United Kingdom. Consecutive children listed for excision of a thyroglossal duct cyst whose parents agreed to participate were included and there were no exclusion criteria. Results: Surgically excised thyroglossal duct cyst or remnant specimens from five patients (two males, three females) were examined using micro-CT alongside traditional histopathological examination. In all cases, micro-CT imaging was able to demonstrate 3D imaging datasets of the specimens successfully and direct radio-pathological comparisons were made (Figures 1-5, Supplementary Video 1). Conclusions: The study has shown the feasibility and utility of post-operative micro-CT imaging of thyroglossal duct cysts specimens as a visual aid to traditional histopathological examination. It better informs the pathological specimen sectioning using multi-planar reconstruction and volume rendering tools without tissue destruction. In the complex, often arborised relationship between a thyroglossal duct cyst and the hyoid, micro-CT provides valuable image plane orientation and indicates proximity of the duct to the surgical margins. This is the first case series to explore the use of micro-CT imaging for pediatric thyroglossal duct specimens and it informs future work investigating the generalizability of micro-CT imaging methods for other lesions, particularly those from the head and neck region where precisely defining margins of excision may be challenging.

Air contrast of the intervillous space enables non-disruptive Micro-CT analysis of paraffin-embedded archival placental tissue

The morphometric parameters of the villous tree are a strong indicator of deviant placentas. Methods have been established to digitally reconstruct small peripheral branches by tracing with 3D Microscopy at subcellular resolution. Micro-CT can help scale up the scanning of villous trees with resolution in the range of a few micrometers. As placental tissue samples are routinely conserved and archived by fixation and paraffin embedding, the villous structures are inaccessible to Micro-CT imaging due to poor contrast between paraffin and paraffinized tissue. We present a novel procedure for contrast enhancement by selectively replacing wax by air in the intervillous space.

MicroCT optimisation for imaging fascicular anatomy in peripheral nerves

BACKGROUND

Due to the lack of understanding of the fascicular organisation, vagus nerve stimulation (VNS) leads to unwanted off-target effects. Micro-computed tomography (microCT) can be used to trace fascicles from periphery and image fascicular anatomy.

NEW METHOD

In this study, we present a simple and reproducible method for imaging fascicles in peripheral nerves with iodine staining and microCT for the determination of fascicular anatomy and organisation.

RESULTS

At the determined optimal pre-processing steps and scanning parameters, the microCT protocol allowed for segmentation and tracking of fascicles within the nerves. This was achieved after 24 hours and 120 hours of staining with Lugol's solution (1% total iodine) for rat sciatic and pig vagus nerves, respectively, and the following scanning parameters: 4 μm voxel size, 35 kVp energy, 114 μA current, 4 W power, 0.25 fps in 4 s exposure time, 3176 projections and a molybdenum target.

COMPARISON WITH EXISTING METHOD(S)

This optimised method for imaging fascicles provides high-resolution, three-dimensional images and full imaging penetration depth not obtainable with methods typically used such as histology, magnetic resonance imaging and optical coherence tomography whilst obviating time-consuming pre-processing methods, the amount of memory required, destruction of the samples and the cost associated with current microCT methods.

CONCLUSION

The optimised microCT protocol facilitates segmentation and tracking of the fascicles within the nerve. The resulting segmentation map of the functional anatomical organisation of the vagus nerve will enable selective VNS ultimately allowing for the avoidance of the off-target effects and improving its therapeutic efficacy.

Comparative analysis of sample preparation protocols of soft biological tissues for morphometric studies using synchrotron-based X-ray microtomography

The spread of microtomography as a tool for visualization of soft tissues has had a significant impact on a better understanding of complex biological systems. This technique allows a detailed three-dimensional quantitative view of the specimen to be obtained, correlating its morphological organization with its function, providing valuable insights on the functionality of the tissue. Regularly overlooked, but of great importance, proper sample mounting and preparation are fundamental for achieving the highest possible image quality even for the high-resolution imaging systems currently under development. Here, a quantitative analysis compares some of the most common sample-mounting strategies used for synchrotron-based X-ray microtomography of soft tissues: alcoholic-immersion, paraffin-embedding and critical-point drying. These three distinct sample-mounting strategies were performed on the same specimen in order to investigate their impact on sample morphology regardless of individual sample variation. In that sense, the alcoholic-immersion strategy, although causing less shrinkage to the tissue, proved to be the most unsuitable approach for a high-throughput high-resolution imaging experiment due to sample drifting. Also, critical-point drying may present some interesting advantages regarding image quality but is also incompatible with a high-throughput experiment. Lastly, paraffin-embedding is shown to be the most suitable strategy for current soft tissue microtomography experiments. Such detailed analysis of biological sample-mounting strategies for synchrotron-based X-ray microtomography are expected to offer valuable insights on the best approach for using this technique for 3D imaging of soft tissues and following morphometric analysis.

Synchrotron-based phase-contrast micro-CT as a tool for understanding pulmonary vascular pathobiology and the 3-D microanatomy of alveolar capillary dysplasia

This study aimed to explore the value of synchrotron-based phase-contrast microcomputed tomography (micro-CT) in pulmonary vascular pathobiology. The microanatomy of the lung is complex with intricate branching patterns. Tissue sections are therefore difficult to interpret. Recruited intrapulmonary bronchopulmonary anastomoses (IBAs) have been described in several forms of pulmonary hypertension, including alveolar capillary dysplasia with misaligned pulmonary veins (ACD/MPV). Here, we examine paraffin-embedded tissue using this nondestructive method for high-resolution three-dimensional imaging. Blocks of healthy and ACD/MPV lung tissue were used. Pulmonary and bronchial arteries in the ACD/MPV block had been preinjected with dye. One section per block was stained, and areas of interest were marked to allow precise beam-alignment during image acquisition at the X02DA TOMCAT beamline (Swiss Light Source). A ×4 magnifying objective coupled to a 20-µm thick scintillating material and a sCMOS detector yielded the best trade-off between spatial resolution and field-of-view. A phase retrieval algorithm was applied and virtual tomographic slices and video clips of the imaged volumes were produced. Dye injections generated a distinct attenuation difference between vessels and surrounding tissue, facilitating segmentation and three-dimensional rendering. Histology and immunohistochemistry post-imaging offered complementary information. IBAs were confirmed in ACD/MPV, and the MPVs were positioned like bronchial veins/venules. We demonstrate the advantages of using synchrotron-based phase-contrast micro-CT for three-dimensional characterization of pulmonary microvascular anatomy in paraffin-embedded tissue. Vascular dye injections add additional value. We confirm intrapulmonary shunting in ACD/MPV and provide support for the hypothesis that MPVs are dilated bronchial veins/venules.

Noninvasive Imaging Biomarker Identifies Small Airway Damage in Severe Chronic Obstructive Pulmonary Disease

Rationale: Evidence suggests damage to small airways is a key pathologic lesion in chronic obstructive pulmonary disease (COPD). Computed tomography densitometry has been demonstrated to identify emphysema, but no such studies have been performed linking an imaging metric to small airway abnormality.Objectives: To correlate ex vivo parametric response mapping (PRM) analysis to in vivo lung tissue measurements of patients with severe COPD treated by lung transplantation and control subjects.Methods: Resected lungs were inflated, frozen, and systematically sampled, generating 33 COPD (n = 11 subjects) and 22 control tissue samples (n = 3 subjects) for micro-computed tomography analysis of terminal bronchioles (TBs; last generation of conducting airways) and emphysema.Measurements and Main Results: PRM analysis was conducted to differentiate functional small airways disease (PRMfSAD) from emphysema (PRMEmph). In COPD lungs, TB numbers were reduced (P = 0.01); surviving TBs had increased wall area percentage (P < 0.001), decreased circularity (P < 0.001), reduced cross-sectional luminal area (P < 0.001), and greater airway obstruction (P = 0.008). COPD lungs had increased airspace size (P < 0.001) and decreased alveolar surface area (P < 0.001). Regression analyses demonstrated unique correlations between PRMfSAD and TBs, with decreased circularity (P < 0.001), decreased luminal area (P < 0.001), and complete obstruction (P = 0.008). PRMEmph correlated with increased airspace size (P < 0.001), decreased alveolar surface area (P = 0.003), and fewer alveolar attachments per TB (P = 0.01).Conclusions: PRMfSAD identifies areas of lung tissue with TB loss, luminal narrowing, and obstruction. This is the first confirmation that an imaging biomarker can identify terminal bronchial pathology in established COPD and provides a noninvasive imaging methodology to identify small airway damage in COPD.

X-ray Micro-Computed Tomography for Nondestructive Three-Dimensional (3D) X-ray Histology

Historically, micro-computed tomography (μCT) has been considered unsuitable for histologic analysis of unstained formalin-fixed, paraffin-embedded soft tissue biopsy specimens because of a lack of image contrast between the tissue and the paraffin. However, we recently demonstrated that μCT can successfully resolve microstructural detail in routinely prepared tissue specimens. Herein, we illustrate how μCT imaging of standard formalin-fixed, paraffin-embedded biopsy specimens can be seamlessly integrated into conventional histology workflows, enabling nondestructive three-dimensional (3D) X-ray histology, the use and benefits of which we showcase for the exemplar of human lung biopsy specimens. This technology advancement was achieved through manufacturing a first-of-kind μCT scanner for X-ray histology and developing optimized imaging protocols, which do not require any additional sample preparation. 3D X-ray histology allows for nondestructive 3D imaging of tissue microstructure, resolving structural connectivity and heterogeneity of complex tissue networks, such as the vascular network or the respiratory tract. We also demonstrate that 3D X-ray histology can yield consistent and reproducible image quality, enabling quantitative assessment of a tissue's 3D microstructures, which is inaccessible to conventional two-dimensional histology. Being nondestructive, the technique does not interfere with histology workflows, permitting subsequent tissue characterization by means of conventional light microscopy-based histology, immunohistochemistry, and immunofluorescence. 3D X-ray histology can be readily applied to a plethora of archival materials, yielding unprecedented opportunities in diagnosis and research of disease.

Correlative 3D Imaging and Microfluidic Modelling of Human Pulmonary Lymphatics using Immunohistochemistry and High-resolution μCT

Lung lymphatics maintain fluid homoeostasis by providing a drainage system that returns fluid, cells and metabolites to the circulatory system. The 3D structure of the human pulmonary lymphatic network is essential to lung function, but it is poorly characterised. Image-based 3D mathematical modelling of pulmonary lymphatic microfluidics has been limited by the lack of accurate and representative image geometries. This is due to the microstructural similarity of the lymphatics to the blood vessel network, the lack of lymphatic-specific biomarkers, the technical limitations associated with image resolution in 3D, and sectioning artefacts present in 2D techniques. We present a method that combines lymphatic specific (D240 antibody) immunohistochemistry (IHC), optimised high-resolution X-ray microfocus computed tomography (μCT) and finite-element mathematical modelling to assess the function of human peripheral lung tissue. The initial results identify lymphatic heterogeneity within and between lung tissue. Lymphatic vessel volume fraction and fractal dimension significantly decreases away from the lung pleural surface (p < 0.001, n = 25 and p < 0.01, n = 20, respectively). Microfluidic modelling successfully shows that in lung tissue the fluid derived from the blood vessels drains through the interstitium into the lymphatic vessel network and this drainage is different in the subpleural space compared to the intralobular space. When comparing lung tissue from health and disease, human pulmonary lymphatics were significantly different across five morphometric measures used in this study (p ≤ 0.0001). This proof of principle study establishes a new engineering technology and workflow for further studies of pulmonary lymphatics and demonstrates for the first time the combination of correlative μCT and IHC to enable 3D mathematical modelling of human lung microfluidics at micrometre resolution.

Pulmonary Acinus: Understanding the Computed Tomography Findings from an Acinar Perspective

The lung acinus is the most distal portion of the airway responsible for the gas exchange. The normal acini are not visible on conventional computed tomography (CT), but the advent of micro-CT improved the understanding of the microarchitecture of healthy acini. The comprehension of the acinar architecture is pivotal for the understanding of CT findings of diseases that involve the acini. Centriacinar emphysema, for example, presents as round areas of low attenuation due to the destruction of the most central acini with compensatory enlargement of proximal acini due to alveolar wall destruction. In pulmonary fibrosis, intralobular septal fibrosis manifests as acinar wall thickening with an overlap of acinar collapse and compensatory dilation of surrounding acini constituting the cystic disease typical of the usual interstitial pneumonia pattern. This is a state-of-the-art review to describe the acinar structure from the micro-CT perspective and display how the comprehension of the acinar structure can aid in the interpretation of its microarchitecture disruption on conventional CT.

X-ray-Based 3D Virtual Histology-Adding the Next Dimension to Histological Analysis

Histology and immunohistochemistry of thin tissue sections have been the standard diagnostic procedure in many diseases for decades. This method is highly specific for particular tissue regions or cells, but mechanical sectioning of the specimens is required, which destroys the sample in the process and can lead to non-uniform tissue deformations. In addition, regions of interest cannot be located beforehand and the analysis is intrinsically two-dimensional. Micro X-ray computed tomography (μCT) on the other hand can provide 3D images at high resolution and allows for quantification of tissue structures, as well as the localization of small regions of interest. These advantages advocate the use of μCT for virtual histology tool with or without subsequent classical histology. This review summarizes the most recent examples of virtual histology and provides currently known possibilities of improving contrast and resolution of μCT. Following a background in μCT imaging, ex vivo staining procedures for contrast enhancement are presented as well as label-free virtual histology approaches and the technologies, which could rapidly advance it, such as phase-contrast CT. Novel approaches such as zoom tomography and nanoparticulate contrast agents will also be considered. The current evidence suggests that virtual histology may present a valuable addition to the workflow of histological analysis, potentially reducing the workload in pathology, refining tissue classification, and supporting the detection of small malignancies.

How high resolution 3-dimensional imaging changes our understanding of postnatal lung development

During the last 10 + years biologically and clinically significant questions about postnatal lung development could be answered due to the application of modern cutting-edge microscopic and quantitative histological techniques. These are in particular synchrotron radiation based X-ray tomographic microscopy (SRXTM), but also ³Helium Magnetic Resonance Imaging, as well as the stereological estimation of the number of alveoli and the length of the free septal edge. First, the most important new finding may be the following: alveolarization of the lung does not cease after the maturation of the alveolar microvasculature but continues until young adulthood and, even more important, maybe reactivated lifelong if needed to rescue structural damages of the lungs. Second, the pulmonary acinus represents the functional unit of the lung. Because the borders of the acini could not be detected in classical histological sections, any investigation of the acini requires 3-dimensional (imaging) methods. Based on SRXTM it was shown that in rat lungs the number of acini stays constant, meaning that their volume increases by a factor of ~ 11 after birth. The latter is very important for acinar ventilation and particle deposition.

Optimising complementary soft tissue synchrotron X-ray microtomography for reversibly-stained central nervous system samples

Synchrotron radiation microtomography (SRμCT) is a nominally non-destructive 3D imaging technique which can visualise the internal structures of whole soft tissues. As a multi-stage technique, the cumulative benefits of optimising sample preparation, scanning parameters and signal processing can improve SRμCT imaging efficiency, image quality, accuracy and ultimately, data utility. By evaluating different sample preparations (embedding media, tissue stains), imaging (projection number, propagation distance) and reconstruction (artefact correction, phase retrieval) parameters, a novel methodology (combining reversible iodine stain, wax embedding and inline phase contrast) was optimised for fast (~12 minutes), high-resolution (3.2-4.8 μm diameter capillaries resolved) imaging of the full diameter of a 3.5 mm length of rat spinal cord. White-grey matter macro-features and micro-features such as motoneurons and capillary-level vasculature could then be completely segmented from the imaged volume for analysis through the shallow machine learning SuRVoS Workbench. Imaged spinal cord tissue was preserved for subsequent histology, establishing a complementary SRμCT methodology that can be applied to study spinal cord pathologies or other nervous system tissues such as ganglia, nerves and brain. Further, our 'single-scan iterative downsampling' approach and side-by-side comparisons of mounting options, sample stains and phase contrast parameters should inform efficient, effective future soft tissue SRμCT experiment design.

Recent developments in 3-D reconstruction and stereology to study the pulmonary vasculature

Alterations of the pulmonary vasculature are an important feature of human lung diseases such as chronic obstructive pulmonary disease, pulmonary hypertension, and bronchopulmonary dysplasia. Experimental studies to investigate the pathogenesis or a therapeutic intervention in animal models of these diseases often require robust, meaningful, and efficient morphometric data that allow for appropriate statistical testing. The gold standard for obtaining such data is design-based stereology. However, certain morphological characteristics of the pulmonary vasculature make the implementation of stereological methods challenging. For example, the alveolar capillary network functions according to the sheet flow principle, thus making unbiased length estimations impossible and requiring other strategies to obtain mechanistic morphometric data. Another example is the location of pathological changes along the branches of the vascular tree. For developmental defects like in bronchopulmonary dysplasia or for pulmonary hypertension, it is important to know whether certain segments of the vascular tree are preferentially altered. This cannot be overcome by traditional stereological methods but requires the combination of a three-dimensional data set and stereology. The present review aims at highlighting the great potential while discussing the major challenges (such as time consumption and data volume) of this combined approach. We hope to raise interest in the potential of this approach and thus stimulate solutions to overcome the existing challenges.

3D Histopathology-a Lung Tissue Segmentation Workflow for Microfocus X-ray-Computed Tomography Scans

Lung histopathology is currently based on the analysis of 2D sections of tissue samples. The use of microfocus X-ray-computed tomography imaging of unstained soft tissue can provide high-resolution 3D image datasets in the range of 2-10 μm without affecting the current diagnostic workflow. Important details of structural features such as the tubular networks of airways and blood vessels are contained in these datasets but are difficult and time-consuming to identify by manual image segmentation. Providing 3D structures permits a better understanding of tissue functions and structural interrelationships. It also provides a more complete picture of heterogeneous samples. In addition, 3D analysis of tissue structure provides the potential for an entirely new level of quantitative measurements of this structure that have previously been based only on extrapolation from 2D sections. In this paper, a workflow for segmenting such 3D images semi-automatically has been created using and extending the ImageJ open-source software and key steps of the workflow have been integrated into a new ImageJ plug-in called LungJ. Results indicate an improved workflow with a modular organization of steps facilitating the optimization for different sample and scan properties with expert input as required. This allows for incremental and independent optimization of algorithms leading to faster segmentation. Representation of the tubular networks in samples of human lung, building on those segmentations, has been demonstrated using this approach.

Small airways disease in mild and moderate chronic obstructive pulmonary disease: a cross-sectional study

BACKGROUND

The concept that small conducting airways less than 2 mm in diameter become the major site of airflow obstruction in chronic obstructive pulmonary disease (COPD) is well established in the scientific literature, and the last generation of small conducting airways, terminal bronchioles, are known to be destroyed in patients with very severe COPD. We aimed to determine whether destruction of the terminal and transitional bronchioles (the first generation of respiratory airways) occurs before, or in parallel with, emphysematous tissue destruction.

METHODS

In this cross-sectional analysis, we applied a novel multiresolution CT imaging protocol to tissue samples obtained using a systematic uniform sampling method to obtain representative unbiased samples of the whole lung or lobe of smokers with normal lung function (controls) and patients with mild COPD (Global Initiative for Chronic Obstructive Lung Disease [GOLD] stage 1), moderate COPD (GOLD 2), or very severe COPD (GOLD 4). Patients with GOLD 1 or GOLD 2 COPD and smokers with normal lung function had undergone lobectomy and pneumonectomy, and patients with GOLD 4 COPD had undergone lung transplantation. Lung tissue samples were used for stereological assessment of the number and morphology of terminal and transitional bronchioles, airspace size (mean linear intercept), and alveolar surface area.

FINDINGS

Of the 34 patients included in this study, ten were controls (smokers with normal lung function), ten patients had GOLD 1 COPD, eight had GOLD 2 COPD, and six had GOLD 4 COPD with centrilobular emphysema. The 34 lung specimens provided 262 lung samples. Compared with control smokers, the number of terminal bronchioles decreased by 40% in patients with GOLD 1 COPD (p=0·014) and 43% in patients with GOLD 2 COPD (p=0·036), the number of transitional bronchioles decreased by 56% in patients with GOLD 1 COPD (p=0·0001) and 59% in patients with GOLD 2 COPD (p=0·0001), and alveolar surface area decreased by 33% in patients with GOLD 1 COPD (p=0·019) and 45% in patients with GOLD 2 COPD (p=0·0021). These pathological changes were found to correlate with lung function decline. We also showed significant loss of terminal and transitional bronchioles in lung samples from patients with GOLD 1 or GOLD 2 COPD that had a normal alveolar surface area. Remaining small airways were found to have thickened walls and narrowed lumens, which become more obstructed with increasing COPD GOLD stage.

INTERPRETATION

These data show that small airways disease is a pathological feature in mild and moderate COPD. Importantly, this study emphasises that early intervention for disease modification might be required by patients with mild or moderate COPD.

FUNDING

Canadian Institutes of Health Research.

3D printing from microfocus computed tomography (micro-CT) in human specimens: education and future implications

Microfocus CT (micro-CT) is an imaging method that provides three-dimensional digital data sets with comparable resolution to light microscopy. Although it has traditionally been used for non-destructive testing in engineering, aerospace industries and in preclinical animal studies, new applications are rapidly becoming available in the clinical setting including post-mortem fetal imaging and pathological specimen analysis. Printing three-dimensional models from imaging data sets for educational purposes is well established in the medical literature, but typically using low resolution (0.7 mm voxel size) data acquired from CT or MR examinations. With higher resolution imaging (voxel sizes below 1 micron, <0.001 mm) at micro-CT, smaller structures can be better characterised, and data sets post-processed to create accurate anatomical models for review and handling. In this review, we provide examples of how three-dimensional printing of micro-CT imaged specimens can provide insight into craniofacial surgical applications, developmental cardiac anatomy, placental imaging, archaeological remains and high-resolution bone imaging. We conclude with other potential future usages of this emerging technique.

Postmortem microfocus computed tomography for early gestation fetuses: a validation study against conventional autopsy

BACKGROUND

Perinatal autopsy provides useful clinical information in up to 40% of cases. However, there is a substantial unmet clinical need with regards to postmortem investigation of early gestation fetal loss for parents for whom standard autopsy is either not available or not acceptable. Parents dislike the invasive nature of autopsy, but current clinical imaging techniques do not provide high-enough imaging resolution in small fetuses. We hypothesized that microfocus computed tomography, which is a rapid high-resolution imaging technique, could give accurate diagnostic imaging after early gestation fetal loss.

OBJECTIVE

The objective of the study was to evaluate the diagnostic accuracy of microfocus computed tomography for noninvasive human fetal autopsy for early gestation fetuses, with the use of conventional autopsy as the reference standard.

STUDY DESIGN

We compared iodinated whole body microfocus computed tomography in 20 prospectively recruited fetuses (11-21 weeks gestation from 2 centers) with conventional autopsy in a double-blinded manner for a main diagnosis and findings in specific body organs. Fetuses were prepared with 10% formalin/potassium tri-iodide. Images were acquired with a microfocus computed tomography scanner with size-appropriate parameters. Images were evaluated independently by 2 pediatric radiologists, who were blinded to formal perinatal autopsy results, across 40 individual indices to reach consensus. The primary outcome was agreement between microfocus computed tomography and conventional autopsy for overall diagnosis.

RESULTS

Postmortem whole body fetal microfocus computed tomography gave noninvasive autopsy in minutes, at a mean resolution of 27μm, with high diagnostic accuracy in fetuses at <22 weeks gestation. Autopsy demonstrated that 13 of 20 fetuses had structural abnormalities, 12 of which were also identified by microfocus computed tomography (92.3%). Overall, microfocus computed tomography agreed with overall autopsy findings in 35 of 38 diagnoses (15 true positive, 18 true negative; sensitivity 93.8% [95% confidence interval, 71.7-98.9%], specificity 100% [95% confidence interval, 82.4-100%]), with 100% agreement for body imaging diagnoses. Furthermore, after removal of nondiagnostic indices, there was agreement for 700 of 718 individual body organ indices that were assessed on microfocus computed tomography and autopsy (agreement, 97.5%; 95% confidence interval, 96.1-98.4%), with no overall differences between fetuses at ≤14 or >14 weeks gestation (agreement, 97.2% and 97.9%, respectively). Within first-trimester fetal loss cases (<14 weeks gestation), microfocus computed tomography analysis yielded significantly fewer nondiagnostic indices than autopsy examination (22/440 vs 48/348, respectively; P<.001).

CONCLUSION

Postmortem whole-body fetal microfocus computed tomography gives noninvasive, detailed anatomic examinations that are achieved in minutes at high resolution. Microfocus computed tomography may be preferable to magnetic resonance imaging in early gestation fetuses and may offer an acceptable method of examination after fetal loss for parents who decline invasive autopsy. This will facilitate autopsy and subsequent discussions between medical professionals who are involved in patient care and counselling for future pregnancies.

Three-dimensional reconstruction of prostate cancer architecture with serial immunohistochemical sections: hallmarks of tumour growth, tumour compartmentalisation, and implications for grading and heterogeneity

AIMS

Conventional morphology of prostate cancer considers only the two-dimensional (2D) architecture of the tumour. Our aim was to examine the feasibility of three-dimensional (3D) reconstruction of tumour morphology based on multiple consecutive histological sections and to decipher relevant features of prostate cancer architecture.

METHODS AND RESULTS

Seventy-five consecutive histological sections (5 μm) of a typical prostate adenocarcinoma (Gleason score of 3 + 4 = 7) were immunostained (pan-cytokeratin) and scanned for further 3D reconstructions with fiji/imagej software. The main findings related to the prostate cancer architecture in this case were: (i) continuity of all glands, with the tumour being an integrated system, even in Gleason pattern 4 with poorly formed glands-no short-range migration of cells by Gleason pattern 4 (poorly formed glands); (ii) no repeated interconnections between the glands, with a tumour building a tree-like branched structure with very 'plastic' branches (maximal depth of investigation 375 μm); (iii) very stark compartmentalisation of the tumour related to extensive branching, the coexistence of independent terminal units of such branches in one 2D slice explaining intratumoral heterogeneity; (iv) evidence of a craniocaudal growth direction in interglandular regions of the prostate and for a lateromedial growth direction in subcapsular posterolateral regions; and (v) a 3D architecture-based description of Gleason pattern 4 with poorly formed glands, and its continuum with Gleason pattern 3.

CONCLUSIONS

Consecutive histological sections provide high-quality material for 3D reconstructions of the tumour architecture, with excellent resolution. The reconstruction of multiple regions in this typical case of a Gleason score 3 + 4 = 7 tumour provides insights into relevant aspects of tumour growth, the continuity of Gleason patterns 3 and 4, and tumour heterogeneity.

Parenchymal Airspace Profiling: Sensitive Quantification and Characterization of Lung Structure Evaluating Parenchymal Destruction

Lung morphometry was introduced over 50 years ago to provide quantitative evaluation of the lung structure. The existing parameters, such as mean linear intercept and destructive index, suffer from simplistic data interpretation and a subjective data acquisition process. To overcome these existing shortcomings, parenchymal airspace profiling (PAP) was developed to provide a more detailed and unbiased quantitative method. Following the standard protocols of fixation, embedding, and sectioning, lung micrographs were: (1) marked with nonparenchymal area, preprocessed, and binarized under the researcher's supervision; (2) analyzed with a statistical learning method, Gaussian mixture model, to provide an unbiased categorization of parenchymal airspace compartments, corresponding to a single alveolus, alveolar sac, and ductal/destructive airspace; and (3) further quantified into morphometric parameters, including reference volume, alveolar count, and ductal/destructive fraction (DF) based on stereological principles. PAP was performed on hematoxylin and eosin-stained lung sections from mice and rabbits. Unbiased categorization revealed differences in alveolar size among several mouse strains (NZW/LacJ<AKR/J<A/J<C57BL/6J) and across species (mouse<rabbit). Further quantification indicates that parenchymal destruction, modeled in mouse lungs with 1-month smoke exposure, resulted in decreased alveolar count, increased DF, but no significant differences in mean linear intercept. DF also provides a robust measurement that is not biased by processing artifacts, magnification, or reference volume, which are common limitations in human lung biopsies or data obtained from different laboratories. PAP is a novel approach to lung morphometry that offers more detailed characterization of the lung structure, sensitivity, and robustness than presently used methods for evaluating parenchymal destruction.

MicroCT analysis of vascular morphometry: a comparison of right lung lobes in the SUGEN/hypoxic rat model of pulmonary arterial hypertension

Pulmonary arterial hypertension (PAH) is a rare disease characterized by significant vascular remodeling within the lung. Clinical computed tomography (CT) scans are routinely used to aid in PAH diagnosis. Animal models, including the Sugen-hypoxic rat model (SU/hyp), of PAH closely mimic human PAH development. We have previously used micro-computed tomography (microCT) to find extensive right lung vascular remodeling in the SU/hyp. We hypothesized that the individual right lung lobes may not contribute equally to overall lung vascular remodeling. Sprague-Dawley rats were subjected to a subcutaneous injection of vascular endothelial growth factor receptor blocker (Sugen 5416) and subsequently exposed to chronic hypoxic conditions (10% O₂) for three weeks. Following perfusion of the lung vasculature with an opaque resin (Microfil), the right lung lobes were microCT-imaged with a 10-µm voxel resolution and 3D morphometry analysis was performed separately on each lobe. As expected, we found a significantly lower ratio of vascular volume to total lobe volume in the SU/hyp compared with the control, but only in the distal lobes (inferior: 0.23 [0.21–0.30] versus 0.35 [0.27–0.43], P = 0.02; accessory: 0.27 [0.25–0.33] versus 0.37 [0.29–0.43], P = 0.06). Overall, we observed significantly fewer continuous blood vessels and reduced vascular density while having greater vascular lumen diameters in the distal lobes of both groups (P < 0.05). In addition, the vascular separation within the SU/hyp lobes and the vascular surface area to volume ratio were significantly greater in the SU/hyp lobes compared with controls (P < 0.03). Results for the examined parameters support the overall extensive vascular remodeling in the SU/hyp model and suggest this may be lobe-dependent.

Early clinical applications for imaging at microscopic detail: microfocus computed tomography (micro-CT)

Microfocus CT (micro-CT) has traditionally been used in industry and preclinical studies, although it may find new applicability in the routine clinical setting. It can provide high-resolution three-dimensional digital imaging data sets to the same level of detail as microscopic examination without the need for tissue dissection. Micro-CT is already enabling non-invasive detailed internal assessment of various tissue specimens, particularly in breast imaging and early gestational fetal autopsy, not previously possible from more conventional modalities such as MRI or CT. In this review, we discuss the technical aspects behind micro-CT image acquisition, how early work with small animal studies have informed our knowledge of human disease and the imaging performed so far on human tissue specimens. We conclude with potential future clinical applications of this novel and emerging technique.

Imaging Invasion: Micro-CT imaging of adamantinomatous craniopharyngioma highlights cell type specific spatial relationships of tissue invasion

Tissue invasion and infiltration by brain tumours poses a clinical challenge, with destruction of structures leading to morbidity. We assessed whether micro-CT could be used to map tumour invasion in adamantinomatous craniopharyngioma (ACP), and whether it could delineate ACPs and their intrinsic components from surrounding tissue.

Three anonymised archival frozen ACP samples were fixed, iodinated and imaged using a micro-CT scanner prior to the use of standard histological processing and immunohistochemical techniques.

We demonstrate that micro-CT imaging can non-destructively give detailed 3D structural information of tumours in volumes with isotropic voxel sizes of 4–6 microns, which can be correlated with traditional histology and immunohistochemistry.

Such information complements classical histology by facilitating virtual slicing of the tissue in any plane and providing unique detail of the three dimensional relationships of tissue compartments.

The Role of Micro-CT in 3D Histology Imaging

OBJECTIVES

3D histology tissue modeling is a useful analytical technique for understanding anatomy and disease at the cellular level. However, the current accuracy of 3D histology technology is largely unknown, and errors, misalignment and missing information are common in 3D tissue reconstruction. We used micro-CT imaging technology to better understand these issues and the relationship between fresh tissue and its 3D histology counterpart.

METHODS

We imaged formalin-fixed and 2% Lugol-stained mouse brain, human uterus and human lung tissue with micro-CT. We then conducted image analyses on the tissues before and after paraffin embedding using 3D Slicer and ImageJ software to understand how tissue changes between the fixation and embedding steps.

RESULTS

We found that all tissue samples decreased in volume by 19.2-61.5% after embedding, that micro-CT imaging can be used to assess the integrity of tissue blocks, and that micro-CT analysis can help to design an optimized tissue-sectioning protocol.

CONCLUSIONS

Micro-CT reference data help to identify where and to what extent tissue was lost or damaged during slide production, provides valuable anatomical information for reconstructing missing parts of a 3D tissue model, and aids in correcting reconstruction errors when fitting the image information in vivo and ex vivo.

Three-dimensional characterization of fibroblast foci in idiopathic pulmonary fibrosis

In idiopathic pulmonary fibrosis (IPF), the fibroblast focus is a key histological feature representing active fibroproliferation. On standard 2D pathologic examination, fibroblast foci are considered small, distinct lesions, although they have been proposed to form a highly interconnected reticulum as the leading edge of a “wave” of fibrosis. Here, we characterized fibroblast focus morphology and interrelationships in 3D using an integrated micro-CT and histological methodology. In 3D, fibroblast foci were morphologically complex structures, with large variations in shape and volume (range, 1.3 × 10⁴ to 9.9 × 10⁷ μm³). Within each tissue sample numerous multiform foci were present, ranging from a minimum of 0.9 per mm³ of lung tissue to a maximum of 11.1 per mm³ of lung tissue. Each focus was an independent structure, and no interconnections were observed. Together, our data indicate that in 3D fibroblast foci form a constellation of heterogeneous structures with large variations in shape and volume, suggesting previously unrecognized plasticity. No evidence of interconnectivity was identified, consistent with the concept that foci represent discrete sites of lung injury and repair.

Integrated histological and microCT analyses reveal that 3D fibroblast foci are discrete structures with marked variations in shape and volume, suggesting previously unrecognized plasticity.