Tissue arrays as fiducial markers for section alignment in 3-D reconstruction technology

Improved image processing for 3D virtual object construction from serial sections reveals tissue patterns in root tips of Zea mays

Premise

Previously we described methods for generating three-dimensional (3D) virtual reconstructions of plant tissues from transverse thin sections. Here, we report the applicability of longitudinal sections and improved image-processing steps that are simpler to perform and utilize free applications.

Methods

In order to obtain improved digital images and a virtual 3D object (cuboid), GIMP 2.10 and ImageJ 2.3.0 running on a laptop computer were used. Sectional views of the cuboid and 3D visualization were realized with use of the plug-ins "Volume Viewer" and "3D Viewer" in ImageJ.

Results

A 3D object was constructed and sectional views along several cutting planes were generated. The 3D object consisted of selected tissues inside the cuboid that were extracted and visualized from the original section data, and an animated video of the 3D construct was also produced.

Discussion

Virtual cuboids can be constructed by stacking longitudinal images along the transverse depth direction or stacking transverse images vertically along the organ axis, with both generating similar 3D objects. Which to use depends on the purpose of the investigation: if the vertical cell structures need close examination, the former method may be better, but for more general spatial evaluations or for evaluation of organs over longer tissue distances than can be accommodated with longitudinal sectioning, the latter method should be chosen.

Micro- and nano-tomography analysis of mouse soleus muscle using radiation

In this study, we analyze radiation images of muscle structure of mice soleus muscles using radiation source-based microtomography and nanotomography. Soleus muscle samples were collected for analysis from 8-week-old male Institute of Cancer Research mice. First, phase-contrast X-ray microtomography was employed in these experiments. Then to obtain images with excellent contrast, imaging was performed using monochromatic light with excellent transmission power. To analyze additional muscle structures in higher magnification images than these images, nanotomography was performed, which facilitated obtaining high-magnification and high-resolution images. Muscle tissue microstructures were confirmed through three-dimensional images obtained from phase-contrast X-ray microtomography. Thus, the muscle tissue's overall shape at microscopic level can be captured. Additionally, a single muscle fiber was examined using hard X-ray nano-imaging, through which we could observe the alignment of countless myofibrils, that is, actin and myosin filaments in the muscle fibers. Thus, the methodology adopted here proved to be advantageous in analyzing the muscle tissue's overall structure with microtomography and in observing the myofibrils in detail using nanotomography.

Vascular Casting of Adult and Early Postnatal Mouse Lungs for Micro-CT Imaging

Blood vessels form intricate networks in 3-dimensional space. Consequently, it is difficult to visually appreciate how vascular networks interact and behave by observing the surface of a tissue. This method provides a means to visualize the complex 3-dimensional vascular architecture of the lung. To accomplish this, a catheter is inserted into the pulmonary artery and the vasculature is simultaneously flushed of blood and chemically dilated to limit resistance. Lungs are then inflated through the trachea at a standard pressure and the polymer compound is infused into the vascular bed at a standard flow rate. Once the entire arterial network is filled and allowed to cure, the lung vasculature may be visualized directly or imaged on a micro-CT (µCT) scanner. When performed successfully, one can appreciate the pulmonary arterial network in mice ranging from early postnatal ages to adults. Additionally, while demonstrated in the pulmonary arterial bed, this method can be applied to any vascular bed with optimized catheter placement and endpoints.

Ex vivo microangioCT: Advances in microvascular imaging

Therapeutic modulation of angiogenesis is believed to be a prospective powerful treatment strategy to modulate the microcirculation and therefore help millions of patients with cardiovascular and cancer diseases. The often-frustrating results from late-stage clinical studies indicate an urgent need for improved assessment of the pro- and anti-angiogenic compounds in preclinical stage of investigation. For such a proper assessment, detailed vascular visualization and adequate quantification are essential. Nowadays, there are few imaging modalities available, but none of them provides non-destructive 3D-visualization of the vasculature down to the capillary level. In many instances, the approaches cannot be combined with the subsequent histological or ultrastructural analysis. In this review, we address the latest developments in the microvascular imaging, namely, the microangioCT approach with a polymer-based contrast agent (μAngiofil). This approach allows time-efficient non-destructive 3D-imaging of the organ and its vasculature including the finest capillaries. Besides the superior visualization, the obtained detailed 3D information on the organ vasculature enables its 3D-skeletonization and further quantitative analysis. Probably the only significant limitation of the described approach is that it can be used only ex vivo, i.e., no longitudinal studies. In spite of this drawback, microangioCT with μAngiofil is a relatively simple and straightforward tool with a broad application range for studying physiological and pathological alterations in the microvasculature of any organ. It provides microvascular imaging at unprecedented level and enables correlative microscopy.

Correlative Imaging of the Murine Hind Limb Vasculature and Muscle Tissue by MicroCT and Light Microscopy

A detailed vascular visualization and adequate quantification is essential for the proper assessment of novel angiomodulating strategies. Here, we introduce an ex vivo micro-computed tomography (microCT)-based imaging approach for the 3D visualization of the entire vasculature down to the capillary level and rapid estimation of the vascular volume and vessel size distribution. After perfusion with μAngiofil^®, a novel polymerizing contrast agent, low- and high-resolution scans (voxel side length: 2.58–0.66 μm) of the entire vasculature were acquired. Based on the microCT data, sites of interest were defined and samples further processed for correlative morphology. The solidified, autofluorescent μAngiofil^® remained in the vasculature and allowed co-registering of the histological sections with the corresponding microCT-stack. The perfusion efficiency of μAngiofil^® was validated based on lectin-stained histological sections: 98 ± 0.5% of the blood vessels were μAngiofil^®-positive, whereas 93 ± 2.6% were lectin-positive. By applying this approach we analyzed the angiogenesis induced by the cell-based delivery of a controlled VEGF dose. Vascular density increased by 426% mainly through the augmentation of medium-sized vessels (20–40 μm). The introduced correlative and quantitative imaging approach is highly reproducible and allows a detailed 3D characterization of the vasculature and muscle tissue. Combined with histology, a broad range of complementary structural information can be obtained.

Early development of the nervous system of the eutherian <i>Tupaia belangeri</i>

Abstract. The longstanding debate on the taxonomic status of Tupaia belangeri (Tupaiidae, Scandentia, Mammalia) has persisted in times of molecular biology and genetics. But way beyond that Tupaia belangeri has turned out to be a valuable and widely accepted animal model for studies in neurobiology, stress research, and virology, among other topics. It is thus a privilege to have the opportunity to provide an overview on selected aspects of neural development and neuroanatomy in Tupaia belangeri on the occasion of this special issue dedicated to Hans-Jürg Kuhn. Firstly, emphasis will be given to the optic system. We report rather "unconventional" findings on the morphogenesis of photoreceptor cells, and on the presence of capillary-contacting neurons in the tree shrew retina. Thereafter, network formation among directionally selective retinal neurons and optic chiasm development are discussed. We then address the main and accessory olfactory systems, the terminal nerve, the pituitary gland, and the cerebellum of Tupaia belangeri. Finally, we demonstrate how innovative 3-D reconstruction techniques helped to decipher and interpret so-far-undescribed, strictly spatiotemporally regulated waves of apoptosis and proliferation which pass through the early developing forebrain and eyes, midbrain and hindbrain, and through the panplacodal primordium which gives rise to all ectodermal placodes. Based on examples, this paper additionally wants to show how findings gained from the reported projects have influenced current neuroembryological and, at least partly, medical research.

Three-dimensional visualization of in vitro cultivated chondrocytes inside porous gelatine scaffolds: A tomographic approach

Synchrotron radiation-based microcomputed tomography (SR-microCT) has become a valuable tool in the structural characterization of different types of materials, achieving volumetric details with micrometre resolution. Biomedical research dealing with porous polymeric biomaterials is one of the research fields which can benefit greatly from the use of SR-microCT. This study demonstrates that current experimental set-ups at synchrotron beamlines achieve a sufficiently high resolution in order to visualize the positions of individual cartilage cells cultivated on porous gelatine scaffolds made by a freeze-structuring technique. Depending on the processing parameters, the pore morphology of the scaffolds investigated was changed from large-pore sized but non-ordered structures to highly directional and fine pored. The cell-seeded scaffolds were stained with a combined Au/Ag stain to enhance the absorption contrast in SR-microCT. While only some cells showed enhanced absorption contrast, most cells did not show any difference in contrast to the surrounding scaffold and were consequently not detectable using conventional greyscale threshold methods. Therefore, using an image-based three-dimensional segmentation tool on the tomographic data revealed a multitude of non-stained cells. In addition, the SR-microCT data were compared with data obtained from scanning electron microscopy, energy dispersive X-ray spectroscopy and histology, while further linking the initial cell density measured via a MTT assay to the pore size as determined by SR-microCT.

Going beyond histology. Synchrotron micro-computed tomography as a methodology for biological tissue characterization: from tissue morphology to individual cells

Current light microscopic methods such as serial sectioning, confocal microscopy or multiphoton microscopy are severely limited in their ability to analyse rather opaque biological structures in three dimensions, while electron optical methods offer either a good three-dimensional topographic visualization (scanning electron microscopy) or high-resolution imaging of very thin samples (transmission electron microscopy). However, sample preparation commonly results in a significant alteration and the destruction of the three-dimensional integrity of the specimen. Depending on the selected photon energy, the interaction between X-rays and biological matter provides semi-transparency of the specimen, allowing penetration of even large specimens. Based on the projection-slice theorem, angular projections can be used for tomographic imaging. This method is well developed in medical and materials science for structure sizes down to several micrometres and is considered as being non-destructive. Achieving a spatial and structural resolution that is sufficient for the imaging of cells inside biological tissues is difficult due to several experimental conditions. A major problem that cannot be resolved with conventional X-ray sources are the low differences in density and absorption contrast of cells and the surrounding tissue. Therefore, X-ray monochromatization coupled with a sufficiently high photon flux and coherent beam properties are key requirements and currently only possible with synchrotron-produced X-rays. In this study, we report on the three-dimensional morphological characterization of articular cartilage using synchrotron-generated X-rays demonstrating the spatial distribution of single cells inside the tissue and their quantification, while comparing our findings to conventional histological techniques.

Histology far away from Flatland: 3D roller-coasting into grade-dependent angiogenetic patterns in oligodendrogliomas

Angiogenesis plays a key role in tumour progression, and undergoes structural changes associated to tumour biology itself. Although vessel density can be easily evaluated in brain tumours using a traditional immuno-histochemical approach, other parameters of conceptual/biological interest, such as the complex patterns of vascular growth, cannot be fully understood using a traditional bi-dimensional evaluation. We use here surgical specimens derived from oligodendrogliomas as a model for a novel elucidative 3D reconstruction of the grade-dependent vascular arborisation in brain tumours.

Surface imaging microscopy using an ultramiller for large volume 3D reconstruction of wax- and resin-embedded tissues

Three-dimensional reconstruction of large tissue volumes using histological thin sections poses difficulties because of registration of sections, section distortion, and the possibility of incomplete data set collection due to section loss. We have constructed an integrated surface imaging system that successfully addresses these problems. Embedded tissue is mounted on a high precision XYZ stage and the upper surface is iteratively: (i) stained to provide an effective optical section, (ii) imaged using a digital camera, and (iii) removed with an ultramiller. This approach provides for the reconstruction of high-quality 3D images by inherently preserving image registration, eliminates section distortion, thus removing the need for complex realignment and correction, and also ensures full capture of all image planes. The system has the capacity to acquire images of tissue structure with voxel sizes from 0.5 to 50 mum over dimensions ranging from micrometers to tens of millimeters. The ultramiller enables large samples to be imaged by reliably removing tissue over their full extent. The ability to visualize key features of 3D tissue structure across such a range of scale and resolution will facilitate the development of a greater understanding of the relationship between structure and function. This understanding is essential for better analyses of the structural changes associated with different disease states, and the development of structure-based computer models of biological function.

Analysis of barley (Hordeum vulgare) grain development using three-dimensional digital models

Analysis of gene expression in the developing barley caryopsis requires effective instruments for visualization of the grain and the 3D expression patterns. Digital models of developing barley (Hordeum vulgare) grains were reconstructed from serial sections to visualize the complex three-dimensional (3D) grain anatomy, to generate and analyse 3D expression patterns, and to quantify tissues during growth. The models provide detailed spatial descriptions of developing grains at anthesis, at the syncytial stage of endosperm development and at the onset of starch accumulation, visualizing and quantifying 18 tissues or tissue complexes. Total caryopsis volumes and volume changes of specific tissues between the stages were determined, and proportions of ovule- and non-ovule-tissues and ratios of filial to maternal tissues were calculated from the model data. To generate and analyse 3D expression patterns, data from mRNA localization by in situ hybridizations were integrated into the models. At the onset of starch accumulation, cell-wall invertase (HvCWINV1) mRNA is mainly localized in the transfer cells and to a lesser degree in zones of the starchy endosperm. Using the model, an expression gradient across the grain was visualized. The expression pattern in the upper region of the caryopsis resembles that found in the median region at an earlier stage, indicating the presence of a developmental gradient. At anthesis, mRNA of the protease nucellin was visualized in a distinct zone of the nucellus near the antipodal cells.

A new vision of tubular and tubulo-lobular carcinomas of the breast, as revealed by 3-D modelling

AIMS

To reveal architectural structure and growth patterns of tubular carcinomas (TC) and tubulo-lobular carcinomas (TLC) of the breast.

METHODS AND RESULTS

We studied a series of 20 pure TC and 22 TLC, evaluating the architectural features of the two entities by bi-dimensional microscopy and by 3-D modelling. We traced the spatial organization of three TCs and three TLCs on serial sections using AE1/AE3 cytokeratin as a marker of the epithelial structures and reconstructed 3-D models of each histological type. The analysis of TC on serial cytokeratin-stained sections showed that the form of the 'tubules' was related to the plane of sectioning and that often they were tear-drop shaped, with a final tail of single cells connecting them together. 3-D models corresponded to a necklace appearance and the tubules of TC appeared as blebs bridging through solid cords to other blebs. In TLC the structure was similar, but the connecting single-cell files were usually longer. Both TC and TLC showed similar E-cadherin positivity and an indolent clinical behaviour.

CONCLUSIONS

TC and TLC share the same architectural and growth patterns and ultimately seem to represent variants of the same tumour type.