From gross anatomy to the nanomorphome: stereological tools provide a paradigm for advancing research in quantitative morphomics

Oral and Parenteral Vaccination against Escherichia coli in Piglets Results in Different Responses

The available E. coli vaccines involve two main types (inactivated and live non-pathogenic) and two routes of administration (oral and parenteral) but the mechanism by which both vaccines and routes of administration work is not yet fully elucidated. The influence of a parenteral vaccine (PV) and an oral one (OV) was studied by analyzing the gene expression of biomarkers indicating cellular infiltration (calprotectin, CAL), tight junction proteins (occludin OCL, and zonulin ZON) that maintain intestinal paracellular integration and two proinflammatory (IFN-γ) and anti-inflammatory (TGF-β) mediator cytokines, as well as histomorphology and IgA production cell density. Differences were observed in CAL, more infiltrated in orally vaccinated animals; OCL also increased in orally vaccinated animals, and higher density of IgA-producing cells in ileum for orally vaccinated groups. Cytokine expression is also different; and there is a lower mRNA for IFN-γ in the parenteral than in the oral vaccinated animals. Finally, the villus height-to-crypt depth ratio was higher in the orally vaccinated groups. The data collectively show clear and different effects derived from the use of each type of vaccine, route of administration and regimen. The results suggest a more rapid and direct effect of oral vaccination and a state of suppression in the absence of a second oral stimulus by the pathogen.

A Stereological Study of the Three Types of Ganglia of Male, Female, and Undifferentiated Scrobicularia plana (Bivalvia)

Neurotransmitters modulate gonadal maturation in bivalves. However, it remains unclear whether there are differences in the nervous system structure between sexes, maturation, and ganglia. Therefore, a stereological study was conducted on the ganglia of adult peppery furrow shell (Scrobicularia plana). Equal-sized males, females, and undifferentiated (gamete absence) animals were fixed with 10% formalin and processed for light microscopy. They were serially cut into 35 µm paraffin thick sections and stained with hematoxylin-eosin. Sections with cerebral (cerebropleural), pedal, and visceral ganglia were studied. The parameters estimated were the volumes of the ganglia, the total and relative volumes of their cortex (outer layer) and medulla (neuropil), and the total number of cells (neurons, glia, and pigmented) per ganglia and compartment. The volumes and numbers were estimated, respectively, by the Cavalieri principle and by the optical fractionator. Females show a larger glia to neuron numerical ratio. Further, females have a greater ganglionic volume than undifferentiated adults, with males showing intermediate values. These facts indicate that the ganglia size is related somehow to maturation. The cell size forms the basis of the differences because total cellularity is equal among the groups. The three ganglion types differ in total volumes and the volume ratio of the cortex versus the medulla. The greater volumes of the pedal ganglia (vis-a-vis the cerebral ones) and of the visceral ganglia (in relation to all others) imply more voluminous cortexes and medullae, but more neuronal and non-neuronal cells only in the visceral. The new fundamental data can help interpret bivalve neurophysiology.

Using virtual microscopy for the development of sampling strategies in quantitative histology and design-based stereology

Only a fraction of specimens under study are usually selected for quantification in histology. Multilevel sampling or tissue probes, slides and fields of view (FOVs) in the regions of interest (ROIs) are required. In general, all parts of the organs under study should be given the same probability to be taken into account; that is, the sampling should be unbiased on all levels. The objective of our study was to provide an overview of the use of virtual microscopy in the context of developing sampling strategies of FOVs for stereological quantification. We elaborated this idea on 18 examples from multiple fields of histology, including quantification of extracellular matrix and muscle tissue, quantification of organ and tumour microvessels and tumour-infiltrating lymphocytes, assessing osseointegration of bone implants, healing of intestine anastomoses and osteochondral defects, counting brain neurons, counting nuclei in vitro cell cultures and others. We provided practical implications for the most common situations, such as exhaustive sampling of ROIs, sampling ROIs of different sizes, sampling the same ROIs for multiple histological methods, sampling more ROIs with variable intensities or using various objectives, multistage sampling and virtual sampling. Recommendations were provided for pilot studies on systematic uniform random sampling of FOVs as a part of optimizing the efficiency of histological quantification to prevent over- or undersampling. We critically discussed the pros and cons of using virtual sections for sampling FOVs from whole scanned sections. Our review demonstrated that whole slide scans of histological sections facilitate the design of sampling strategies for quantitative histology.

A Deep Learning Approach for Segmentation, Classification, and Visualization of 3-D High-Frequency Ultrasound Images of Mouse Embryos

Segmentation and mutant classification of high-frequency ultrasound (HFU) mouse embryo brain ventricle (BV) and body images can provide valuable information for developmental biologists. However, manual segmentation and identification of BV and body requires substantial time and expertise. This article proposes an accurate, efficient and explainable deep learning pipeline for automatic segmentation and classification of the BV and body. For segmentation, a two-stage framework is implemented. The first stage produces a low-resolution segmentation map, which is then used to crop a region of interest (ROI) around the target object and serve as the probability map of the autocontext input for the second-stage fine-resolution refinement network. The segmentation then becomes tractable on high-resolution 3-D images without time-consuming sliding windows. The proposed segmentation method significantly reduces inference time (102.36-0.09 s/volume ≈ 1000× faster) while maintaining high accuracy comparable to previous sliding-window approaches. Based on the BV and body segmentation map, a volumetric convolutional neural network (CNN) is trained to perform a mutant classification task. Through backpropagating the gradients of the predictions to the input BV and body segmentation map, the trained classifier is found to largely focus on the region where the Engrailed-1 (En1) mutation phenotype is known to manifest itself. This suggests that gradient backpropagation of deep learning classifiers may provide a powerful tool for automatically detecting unknown phenotypes associated with a known genetic mutation.

Assessment of Vineyard Canopy Characteristics from Vigour Maps Obtained Using UAV and Satellite Imagery

Canopy characterisation is a key factor for the success and efficiency of the pesticide application process in vineyards. Canopy measurements to determine the optimal volume rate are currently conducted manually, which is time-consuming and limits the adoption of precise methods for volume rate selection. Therefore, automated methods for canopy characterisation must be established using a rapid and reliable technology capable of providing precise information about crop structure. This research providedregression models for obtaining canopy characteristics of vineyards from unmanned aerial vehicle (UAV) and satellite images collected in three significant growth stages. Between 2018 and 2019, a total of 1400 vines were characterised manually and remotely using a UAV and a satellite-based technology. The information collected from the sampled vines was analysed by two different procedures. First, a linear relationship between the manual and remote sensing data was investigated considering every single vine as a data point. Second, the vines were clustered based on three vigour levels in the parcel, and regression models were fitted to the average values of the ground-based and remote sensing-estimated canopy parameters. Remote sensing could detect the changes in canopy characteristics associated with vegetation growth. The combination of normalised differential vegetation index (NDVI) and projected area extracted from the UAV images is correlated with the tree row volume (TRV) when raw point data were used. This relationship was improved and extended to canopy height, width, leaf wall area, and TRV when the data were clustered. Similarly, satellite-based NDVI yielded moderate coefficients of determination for canopy width with raw point data, and for canopy width, height, and TRV when the vines were clustered according to the vigour. The proposed approach should facilitate the estimation of canopy characteristics in each area of a field using a cost-effective, simple, and reliable technology, allowing variable rate application in vineyards.

Mitochondria: A worthwhile object for ultrastructural qualitative characterization and quantification of cells at physiological and pathophysiological states using conventional transmission electron microscopy

Mitochondria are highly dynamic intracellular organelles with ultrastructural heterogeneity reflecting the behaviour and functions of the cells. The ultrastructural remodelling, performed by the counteracting active processes of mitochondrial fusion and fission, enables the organelles to respond to diverse cellular requirements and cues. It is also an important part of mechanisms underlying adaptation of mitochondria to pathophysiological conditions that challenge the cell homeostasis. However, if the stressor is constantly acting, the adaptive capacity of the cell can be exceeded and defective changes in mitochondrial morphology (indicating the insufficient functionality of mitochondria or development of mitochondrial disorders) may appear. Beside qualitative description of mitochondrial ultrastructure, stereological principles concerning the estimation of alterations in mitochondrial volume density or surface density are invaluable approaches for unbiased quantification of cells under physiological or pathophysiological conditions. In order to improve our understanding of cellular functions and dysfunctions, transmission electron microscopy (TEM) still remains a gold standard for qualitative and quantitative ultrastructural examination of mitochondria from various cell types, as well as from those experienced to different stimuli or toxicity-inducing factors. In the current study, general morphological and functional features of mitochondria, and their ultrastructural heterogeneity related to physiological and pathophysiological states of the cells are reviewed. Moreover, stereological approaches for accurate quantification of mitochondrial ultrastructure from electron micrographs taken from TEM are described in detail.

Measuring lysosomal size and frequency by electron microscopy

Changes in size and abundance of late endocytic and autophagic organelles are increasingly appreciated as highly indicative of the physiological or pathological conditions of cells. Electron microscopy (EM) is unsurpassed in high-resolution imaging of both ultrastructural and immunocytochemical features of subcellular compartments. EM-based morphometry permits precise quantitative analyses of organelles, especially after state-of-the-art cryopreparation. Here described step-by-step protocols cover (i) different approaches for sample preparation of almost any specimen, (ii) tools to identify and characterize classes or subpopulations of lysosomes and related organelles, and (iii) convenient, straightforward ways for manual, thus, non-automated measurements of globular or spheroid-shaped organelles.

Stereology as the 3D tool to quantitate lung architecture

Stereology is the method of choice for the quantitative assessment of biological objects in microscopy. It takes into account the fact that, in traditional microscopy such as conventional light and transmission electron microscopy, although one has to rely on measurements on nearly two-dimensional sections from fixed and embedded tissue samples, the quantitative data obtained by these measurements should characterize the real three-dimensional properties of the biological objects and not just their “flatland” appearance on the sections. Thus, three-dimensionality is a built-in property of stereological sampling and measurement tools. Stereology is, therefore, perfectly suited to be combined with 3D imaging techniques which cover a wide range of complementary sample sizes and resolutions, e.g. micro-computed tomography, confocal microscopy and volume electron microscopy. Here, we review those stereological principles that are of particular relevance for 3D imaging and provide an overview of applications of 3D imaging-based stereology to the lung in health and disease. The symbiosis of stereology and 3D imaging thus provides the unique opportunity for unbiased and comprehensive quantitative characterization of the three-dimensional architecture of the lung from macro to nano scale.

Discovery of os cordis in the cardiac skeleton of chimpanzees (Pan troglodytes)

Cardiovascular diseases, especially idiopathic myocardial fibrosis, is one of the most significant causes of morbidity and mortality in captive great apes. This study compared the structure and morphology of 16 hearts from chimpanzees (Pan troglodytes) which were either healthy or affected by myocardial fibrosis using X-ray microtomography. In four hearts, a single, hyperdense structure was detected within the right fibrous trigone of the cardiac skeleton. High resolution scans and histopathology revealed trabecular bones in two cases, hyaline cartilage in another case and a focus of mineralised fibro-cartilaginous metaplasia with endochondral ossification in the last case. Four other animals presented with multiple foci of ectopic calcification within the walls of the great vessels. All hearts affected by marked myocardial fibrosis presented with bone or cartilage formation, and increased collagen levels in tissues adjacent to the bone/cartilage, while unaffected hearts did not present with os cordis or cartilago cordis. The presence of an os cordis has been described in some ruminants, camelids, and otters, but never in great apes. This novel research indicates that an os cordis and cartilago cordis is present in some chimpanzees, particularly those affected by myocardial fibrosis, and could influence the risk of cardiac arrhythmias and sudden death.

Computed Tomography Evidence of Psoas Muscle Atrophy Without Concomitant Tendon Wasting in Early Sepsis

BACKGROUND

Morphomic studies have demonstrated a correlation between sarcopenia and clinical outcomes in septic patients. However, tendon morphomics has not yet been studied in this context. The purpose of the present study was to evaluate tendon morphology in septic patients through analytic morphomics. We hypothesized that morphomic analyses would reveal concomitant muscle and tendon wasting in sepsis patients. The results of this study may help to implement different rehabilitation modalities for critically ill patients.

MATERIALS AND METHODS

The volume and fat content of bilateral psoas muscles and tendons were measured on abdominal computed tomography scans of 25 ICU septic and 25 control trauma patients admitted to the University of Michigan between 2011 and 2012. Univariate and multivariate analyses were performed to determine the relationship between psoas muscle and tendon morphometric data, and the association with clinical variables such as smoking and comorbidities.

RESULTS

Average psoas muscle volume was 12.21 ± 5.6 cm³ for control patients and 9.318 ± 3.3 cm³ in septic patients (P = 0.0023). The average psoas muscle/fat ratio for septic patients was 0.0288 ± 0.071 cm³, compared with 0.0107 ± 0.008 cm³ in the control group (P = 0.075). Average tendon volume in the septic population (0.508 ± 0.191 cm³) was not different than the control cohort (0.493 ± 0.182 cm³) (P = 0.692).

CONCLUSIONS

Our results demonstrate significantly smaller psoas muscle volume in septic patients than in age-, gender-, and BMI-matched trauma patients but no demonstrable change in tendon morphology between patient groups. These findings begin to define the boundaries of clinical application within the field of morphomics.

Personalized medicine: Enhancing our understanding of pediatric growth with analytic morphomics

BACKGROUND/PURPOSE

Analytic morphomics is being used to identify 3-D biologic measures with superior clinical utility and risk stratification over traditional factors such as age, height, and weight. The purpose of this study is to define age and gender specific Pediatric Reference Analytic Morphomics Population (PRAMP™) growth charts.

METHODS

This retrospective study population contains 2591 individual CT scans of a normative reference population of males and females (1-20years old). Growth curves were constructed at the 5th, 25th, 50th, 75th, and 95th quantiles for morphomic variables, including psoas muscle area, trabecular bone density, and visceral fat area by age and gender.

RESULTS

Total psoas muscle area increases over time until late adolescence. Trabecular bone density remains stable until adolescence, decreases during adolescence, and increases in young adulthood. Visceral fat area increases over time with greater variation between the 5th and 95th percentile with increasing age.

CONCLUSIONS

The PRAMP™ data have been used to construct age- and sex-specific reference growth curves. This may be used to better define "abnormal" in efforts to create unique risk-categorization algorithms specific to particular clinical and global health investigations.

LEVEL OF EVIDENCE

Level II.

Quantifying Golgi structure using EM: combining volume-SEM and stereology for higher throughput

Investigating organelles such as the Golgi complex depends increasingly on high-throughput quantitative morphological analyses from multiple experimental or genetic conditions. Light microscopy (LM) has been an effective tool for screening but fails to reveal fine details of Golgi structures such as vesicles, tubules and cisternae. Electron microscopy (EM) has sufficient resolution but traditional transmission EM (TEM) methods are slow and inefficient. Newer volume scanning EM (volume-SEM) methods now have the potential to speed up 3D analysis by automated sectioning and imaging. However, they produce large arrays of sections and/or images, which require labour-intensive 3D reconstruction for quantitation on limited cell numbers. Here, we show that the information storage, digital waste and workload involved in using volume-SEM can be reduced substantially using sampling-based stereology. Using the Golgi as an example, we describe how Golgi populations can be sensed quantitatively using single random slices and how accurate quantitative structural data on Golgi organelles of individual cells can be obtained using only 5–10 sections/images taken from a volume-SEM series (thereby sensing population parameters and cell–cell variability). The approach will be useful in techniques such as correlative LM and EM (CLEM) where small samples of cells are treated and where there may be variable responses. For Golgi study, we outline a series of stereological estimators that are suited to these analyses and suggest workflows, which have the potential to enhance the speed and relevance of data acquisition in volume-SEM.

Lung morphometry: the link between structure and function

The study of the structural basis of gas exchange function in the lung depends on the availability of quantitative information that concerns the structures establishing contact between the air in the alveoli and the blood in the alveolar capillaries, which can be entered into physiological equations for predicting oxygen uptake. This information is provided by morphometric studies involving stereological methods and allows estimates of the pulmonary diffusing capacity of the human lung that agree, in experimental studies, with the maximal oxygen consumption. The basis for this "machine lung" structure lies in the complex design of the cells building an extensive air-blood barrier with minimal cell mass.

Using electron microscopes to look into the lung

In the nineteenth century, there was a dispute about the existence of a lung alveolar epithelium which remained unsolved until the invention of electron microscopy (EM) and its application to the lung. From the early 1960s, Ewald Weibel became the master of lung EM. He showed that the alveolar epithelium is covered with a lining layer containing surfactant. Weibel also explained the phenomenon of "non-nucleated plates" observed already in 1881 by Albert Kölliker. Weibel's most significant contribution was to the development of stereological methods. Therefore, quantitative characterization of lung structure revealing structure-function relationships became possible. Today, the spectrum of EM methods to study the fine structure of the lung has been extended significantly. Cryo-preparation techniques are available which are necessary for immunogold labeling of molecules. Energy-filtering techniques can be used for the detection of elements. There have also been major improvements in stereology, thus providing a very versatile toolbox for quantitative lung phenotype analyses. A new dimension was added by 3D EM techniques. Depending on the desired sample size and resolution, the spectrum ranges from array tomography via serial block face scanning EM and focused ion beam scanning EM to electron tomography. These 3D datasets provide new insights into lung ultrastructure. Biomedical EM is an ever-developing field. Its high resolution remains unparalleled. Moreover, EM has the unique advantage of providing an "open view" into cells and tissues within their full architectural context. Therefore, EM will remain an indispensable tool for a better understanding of the lung's functional design.