Three-dimensional visualisation of soft biological structures by X-ray computed micro-tomography

Porcine in vitro digestion and matrix structure of undigested residue of xylanase- and cellulase-supplemented maize and wheat

BACKGROUND

This study investigated the effects of supplementing maize and wheat with a combination of xylanase and cellulase on porcine in vitro digestibility, nonstarch polysaccharides (NSP) solubilization, and matrix structure. The latter was assessed using synchrotron-based micro-computed tomography (SR-μCT) and Fourier transform mid-infrared (FTMIR) spectroscopy after porcine in vitro degradation. Cereal grains were subjected to porcine in vitro digestion with or without enzyme supplementation (20 000 U kg-1 of each enzyme) in a 2 × 2 factorial design.

RESULTS

In vitro dry matter digestibility (IVDDM) was lower for maize than for wheat (P < 0.05), and enzyme supplementation had no effect on IVDDM. Supplemental enzymes reduced arabinoxylan content in the undigested residue of wheat (53 vs 46 g kg-1, P < 0.05) but not maize (42 vs 44 g kg⁻¹; P > 0.05). Synchrotron-based micro-computed tomography imaging revealed aleurone cells with intact content in the undigested residue of both maize and wheat, regardless of enzyme supplementation. Some endosperm cells in undigested maize residue retained their content, whereas nearly all endosperm cells in undigested enzyme-unsupplemented wheat residue were empty. No endosperm cells were detected in undigested enzyme-supplemented wheat residue. Fourier transform mid-infrared imaging indicated a higher presence of phenolic compounds in maize cell walls than in wheat.

CONCLUSION

Supplemental enzymes did not affect IVDDM for wheat, as they primarily degraded endosperm cell walls, the content of which was already released by pepsin and pancreatin digestion. Similarly, IVDDM for maize remained unaffected, which was probably due to the high phenolic content of its cell walls. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Exploring aortic stiffness in aging mice: a comprehensive methodological overview

Stiffening of the vascular network is associated with the early stages of vascular aging, leading to cardiovascular disorders (hypertension), renal failures, or neurodegenerative diseases (Alzheimer's). Unfortunately, many people remain undiagnosed because diagnostic methods are either unsuitable for a large population or unfamiliar to clinicians which favor the hypertension evaluation. In preclinical research, stiffness studies are often partially conducted. We think that the evaluation of aortic stiffness is essential as it would improve our understanding of aging diseases progression. We propose here a systematic method using decision trees in a multi-scale and multimodal approaches. Our method was evaluated by analyzing the aortic situation in old and young mice. We demonstrate that both the endothelial and smooth muscle cells exhibit pronounced functional alterations in favor of constriction. Additionally, there is significant remodeling of the extracellular matrix, leading to a drastic degradation of elastic fibers and the accumulation of collagen in the aortic wall. This series of changes contributes to the development of vascular rigidity, a preliminary stage of arterial hypertension. Our results suggest that our method should improve preclinical understanding and encourage clinicians to equip themselves with tools for assessing vascular function, as it is an essential issue for preventing numerous pathologies.

Exploring swine oviduct anatomy through micro-computed tomography: a 3D modeling perspective

The oviduct plays a crucial role in the reproductive process, serving as the stage for fertilization and the early stages of embryonic development. When the environment of this organ has been mimicked, it has been shown to enhance in vitro embryo epigenetic reprogramming and to improve the yield of the system. This study explores the anatomical intricacies of two oviduct regions, the uterotubal junction (UTJ) and the ampullary-isthmic junction (AIJ) by using micro-computed tomography (MicroCT). In this study, we have characterized and 3D-reconstructed the oviduct structure, by measuring height and width of the oviduct's folds, along with the assessments of fractal dimension, lacunarity and shape factor. Results indicate distinct structural features in UTJ and AIJ, with UTJ displaying small, uniformly distributed folds and high lacunarity, while AIJ shows larger folds with lower lacunarity. Fractal dimension analysis reveals values for UTJ within 1.189-1.1779, while AIJ values range from 1.559-1.770, indicating differences in structural complexity between these regions. Additionally, blind sacs or crypts are observed, akin to those found in various species, suggesting potential roles in sperm sequestration or reservoir formation. These morphological differences align with functional variations and are essential for developing an accurate 3D model. In conclusion, this research provides information about the oviduct anatomy, leveraging MicroCT technology for detailed 3D reconstructions, which can significantly contribute to the understanding of geometric-morphological characteristics influencing functional traits, providing a foundation for a biomimetic oviduct-on-a-chip.

Visualization of rat tendon in three dimensions using micro-Computed Tomography

Micro-computed tomography (CT) is an X-ray-based imaging modality that produces three-dimensional (3D), high-resolution images of whole-mount tissues, but is typically limited to dense tissues, such as bone. The X-rays readily pass-through tendons, rendering them transparent. Contrast-enhancing chemical stains have been explored, but their use to improve contrast in different tendon types and across developmental stages for micro-CT imaging has not been systematically evaluated. Therefore, we investigated how phosphotungstic acid (PTA) staining and tissue hydration impacts tendon contrast for micro-CT imaging. We showed that PTA staining increased X-ray absorption of tendon to enhance tissue contrast and obtain 3D micro-CT images of immature (postnatal day 21) and sexually mature (postnatal day 50) rat tendons within the tail and hindlimb. Further, we demonstrated that tissue hydration state following PTA staining significantly impacts soft tissue contrast. Using this method, we also found that tail tendon fascicles appear to cross between fascicle bundles. Ultimately, contrast-enhanced 3D micro-CT imaging will lead to better understanding of tendon structure, and relationships between the bone and soft tissues.•Simple tissue fixation and staining technique enhances soft tissue contrast for tendon visualization using micro-CT.•3D tendon visualization in situ advances understanding of musculoskeletal tissue structure and organization.

Detection of nephrocalcinosis using ultrasonography, micro-computed tomography, and histopathology in cats

BACKGROUND

Identification of nephrocalcinosis in cats with chronic kidney disease (CKD) is of clinical interest but the ability of ultrasonography to detect nephrocalcinosis is uncertain.

OBJECTIVES

To compare ultrasonography, micro-computed tomography (μCT) and histopathology for identification of nephrocalcinosis.

ANIMALS

Twelve kidneys from 7 euthyroid client-owned cats with CKD.

METHODS

Descriptive study. Renal ultrasonography was performed ante-mortem for nephrocalcinosis detection. Kidneys were grouped based on nephrocalcinosis: present, suspected, or absent. When cats died, necropsy was performed. Renal tissue was evaluated using μCT for macroscopic nephrocalcinosis, and nephrocalcinosis volume-to-kidney tissue ratio (macro-VN:KT) and sagittal nephrocalcinosis area-to-kidney tissue ratio (macro-AN:KT) were calculated. Each kidney subsequently was bisected longitudinally, formalin-fixed, and paraffin-embedded for microscopic nephrocalcinosis assessment using von Kossa and Alizarin red staining with AN:KT (VK-micro-AN:KT and AR-micro-AN:KT) quantified using ImageJ. Data are presented as median (range). Relationships between macroscopic and microscopic AN:KT were assessed using Spearman's correlation.

RESULTS

Nephrocalcinosis by ultrasonography was considered to be absent in 3, suspected in 3, and present in 5 kidneys; 1 kidney had nephrolithiasis with nephrocalcinosis. The macro-VN:KT was 0.001%, 0.001%, and 0.019%, and the macro-AN:KT was 0.08%, 0.30%, and 1.47%, respectively. Histologically, VK-micro-AN:KT was 0.21%, 2.85%, and 4.56%, and AR-micro-AN:KT was 1.73%, 5.82%, and 8.90% for kidneys where ultrasonographic macro-nephrocalcinosis was absent, suspected, or present, respectively. A strong correlation was identified between macroscopic (macro-AN:KT) and microscopic (VK-micro-AN:KT) nephrocalcinosis (rs = 0.76; P = .01).

CONCLUSIONS AND CLINICAL IMPORTANCE

Ultrasonographically diagnosed nephrocalcinosis correlates well with macroscopic and microscopic nephrocalcinosis at necropsy despite their separation in time.

Calcitriol combined with high-calcium and high-phosphorus diet induces vascular calcification model in chronic kidney disease rats

BACKGROUND

Cardiovascular diseases represent a significant complication arising from chronic kidney disease (CKD). Vascular calcification is an important risk factor for cardiovascular diseases. Reducing vascular calcification is therefore critical to reducing mortality in CKD patients.

HYPOTHESIS

This study aims to establish a vascular calcification model in rats with CKD by administering subcutaneous injections of calcitriol in combination with a high-calcium and high-phosphorus diet.

METHODS

The rats were divided into the CKD vascular calcification model group (subtotal nephrectomy+ [SNx+]) and the sham-operated control group (subtotal nephrectomy- [SNx-]). The rats in the SNx(+) group were administered high-calcium and high-phosphorus feeds following a 5/6 nephrectomy. Calcitriol (1 μg/kg, three times a week) was injected subcutaneously at weeks 0, 4, 8, and 12 after the operation. Measurements of body weight, urine, serum biochemical indicators and vascular calcification level were conducted in rats.

RESULTS

(1) Compared with the SNx(-) group, rats in the SNx(+) group experienced an increase in 24-h urine output, urinary phosphorus, and urinary microprotein excretion, along with the development of severe anemia. Additionally, there was a notable elevation in serum phosphorus, blood urea nitrogen, blood creatinine, fibroblast growth factor 23 (FGF-23), and intact parathyroid hormone levels, accompanied by severe hypoproteinemia at week 12. (2) The results of micro-compuyed tomography (μCT) and alizarin S staining of the thoracic aorta demonstrated an increase in vascular calcification in the SNx(+) group. (3) The expression levels of vascular calcification-related proteins were increased.

CONCLUSIONS

The administration of calcitriol combined with a high-calcium and high-phosphorus diet was found to induce vascular calcification in CKD rats, leading to a disturbance in mineral metabolism. Vascular calcification was effectively induced in CKD rats after 12 weeks of modeling, thereby presenting a novel approach for establishing a vascular calcification model in CKD rats, helping to elucidate this clinical condition and its underlying molecular mechanisms.

Radiopaque Iodosilane-Coated Lipid Hybrid Nanoparticle Contrast Agent for Dual-Modality Ultrasound and X-ray Bioimaging

Here, we report the synthesis of robust hybrid iodinated silica-lipid nanoemulsions (HSLNEs) for use as a contrast agent for ultrasound and X-ray applications. We engineered iodinated silica nanoparticles (SNPs), lipid nanoemulsions, and a series of HSLNEs by a low-energy spontaneous nanoemulsification process. The formation of a silica shell requires sonication to hydrolyze and polymerize/condensate the iodomethyltrimethoxysilane at the oil/water interface of the nanoemulsion droplets. The resulting nanoemulsions (NEs) exhibited a homogeneous spherical morphology under transmission electron microscopy. The particles had diameters ranging from 20 to 120 nm with both negative and positive surface charges in the absence and presence of cetyltrimethylammonium bromide (CTAB), respectively. Unlike CTAB-coated nanoformulations, the CTAB-free NEs showed excellent biocompatibility in murine RAW macrophages and human U87-MG cell lines in vitro. The maximum tolerated dose assessment was evaluated to verify their safety profiles in vivo. In vitro X-ray and ultrasound imaging and in vivo computed tomography were used to monitor both iodinated SNPs and HSLNEs, validating their significant contrast-enhancing properties and suggesting their potential as dual-modality clinical agents in the future.

Current strategies with implementation of three-dimensional cell culture: the challenge of quantification

From growing cells in spheroids to arranging them on complex engineered scaffolds, three-dimensional cell culture protocols are rapidly expanding and diversifying. While these systems may often improve the physiological relevance of cell culture models, they come with technical challenges, as many of the analytical methods used to characterize traditional two-dimensional (2D) cells must be modified or replaced to be effective. Here we review the advantages and limitations of quantification methods based either on biochemical measurements or microscopy imaging. We focus on the most basic of parameters that one may want to measure, the number of cells. Precise determination of this number is essential for many analytical techniques where measured quantities are only meaningful when normalized to the number of cells (e.g. cytochrome p450 enzyme activity). Thus, accurate measurement of cell number is often a prerequisite to allowing comparisons across different conditions (culturing conditions or drug and treatment screening) or between cells in different spatial states. We note that this issue is often neglected in the literature with little or no information given regarding how normalization was performed, we highlight the pitfalls and complications of quantification and call for more accurate reporting to improve reproducibility.

Bayesian inference on a microstructural, hyperelastic model of tendon deformation

Microstructural models of soft-tissue deformation are important in applications including artificial tissue design and surgical planning. The basis of these models, and their advantage over their phenomenological counterparts, is that they incorporate parameters that are directly linked to the tissue's microscale structure and constitutive behaviour and can therefore be used to predict the effects of structural changes to the tissue. Although studies have attempted to determine such parameters using diverse, state-of-the-art, experimental techniques, values ranging over several orders of magnitude have been reported, leading to uncertainty in the true parameter values and creating a need for models that can handle such uncertainty. We derive a new microstructural, hyperelastic model for transversely isotropic soft tissues and use it to model the mechanical behaviour of tendons. To account for parameter uncertainty, we employ a Bayesian approach and apply an adaptive Markov chain Monte Carlo algorithm to determine posterior probability distributions for the model parameters. The obtained posterior distributions are consistent with parameter measurements previously reported and enable us to quantify the uncertainty in their values for each tendon sample that was modelled. This approach could serve as a prototype for quantifying parameter uncertainty in other soft tissues.

p21-/- Mice Exhibit Spontaneous Articular Cartilage Regeneration Post-Injury

OBJECTIVE

Recent studies have implicated the cyclin dependent kinase inhibitor, p21, in enhanced tissue regeneration observed in MRL/MpJ "super-healer" mice. Specifically, p21 is downregulated in MRL cells and similar ear hole closure to MRL mice has been observed in p21^-/- mice. However, the direct implications of p21 deletion in endogenous articular cartilage regeneration remain unknown. In this study, we investigated the role of p21 deletion in the ability of mice to heal full-thickness cartilage defects (FTCDs).

DESIGN

C57BL/6 and p21^-/- (Cdkn1a^tm1Tyj) mice were subjected to FTCD and assessment of cartilage healing was performed at 1 hour, 3 days, 1 week, 2 weeks, and 4 weeks post-FTCD using a 14-point histological scoring system. X-ray microscopy was used to quantify cartilage healing parameters (e.g., cartilage thickness, surface area/volume) between C57BL/6 and p21^-/- mice.

RESULTS

Absence of p21 resulted in increased spontaneous articular cartilage regeneration by 3 days post-FTCD. Furthermore, p21^-/- mice presented with increased cartilage thickness at 1 and 2 weeks post-FTCD compared with uninjured controls, returning to baseline by 4 weeks post-FTCD.

CONCLUSIONS

We report that p21^-/- mice display enhanced articular cartilage regeneration post-FTCD compared with C57BL/6 mice. Furthermore, cartilage thickness was increased in p21^-/- mice at 1 week post-FTCD compared with uninjured p21^-/- mice and C57BL/6 mice.

X-ray microtomography reveals a lattice-like network within aortic elastic lamellae

The arterial wall consists of three concentric layers: intima, media, and adventitia. Beyond their resident cells, these layers are characterized by an extracellular matrix (ECM), which provides both biochemical and mechanical support. Elastin, the major component of arterial ECM, is present in the medial layer and organized in concentric elastic lamellae that confer resilience to the wall. We explored the arterial wall structures from C57Bl6 (control), db/db (diabetic), and ApoE^-/- (atherogenic) mice aged 3 months using synchrotron X-ray computed microtomography on fixed and unstained tissues with a large image field (8 mm³ ). This approach combined a good resolution (0.83 µm/voxel), large 3D imaging field. and an excellent signal to noise ratio conferred by phase-contrast imaging. We determined from 2D virtual slices that the thickness of intramural ECM structures was comparable between strains but automated image analysis of the 3D arterial volumes revealed a lattice-like network within concentric elastic lamellae. We hypothesize that this network could play a role in arterial mechanics. This work demonstrates that phase-contrast synchrotron X-ray computed microtomography is a powerful technique which to characterize unstained soft tissues.

A micro-CT-based standard brain atlas of the bumblebee

In recent years, bumblebees have become a prominent insect model organism for a variety of biological disciplines, particularly to investigate learning behaviors as well as visual performance. Understanding these behaviors and their underlying neurobiological principles requires a clear understanding of brain anatomy. Furthermore, to be able to compare neuronal branching patterns across individuals, a common framework is required, which has led to the development of 3D standard brain atlases in most of the neurobiological insect model species. Yet, no bumblebee 3D standard brain atlas has been generated. Here we present a brain atlas for the buff-tailed bumblebee Bombus terrestris using micro-computed tomography (micro-CT) scans as a source for the raw data sets, rather than traditional confocal microscopy, to produce the first ever micro-CT-based insect brain atlas. We illustrate the advantages of the micro-CT technique, namely, identical native resolution in the three cardinal planes and 3D structure being better preserved. Our Bombus terrestris brain atlas consists of 30 neuropils reconstructed from ten individual worker bees, with micro-CT allowing us to segment neuropils completely intact, including the lamina, which is a tissue structure often damaged when dissecting for immunolabeling. Our brain atlas can serve as a platform to facilitate future neuroscience studies in bumblebees and illustrates the advantages of micro-CT for specific applications in insect neuroanatomy.

A Preliminary Investigation into the Use of Edge Illumination X-ray Phase Contrast Micro-CT for Preclinical Imaging

Purpose

To enable a preliminary assessment of the suitability of edge illumination (EI) x-ray phase contrast (XPC) micro x-ray computed tomography (micro-CT) to preclinical imaging. Specifically, to understand how different acquisition schemes and their combination with dedicated data processing affect contrast-to-noise ratio (CNR) and spatial resolution, while providing control over scan time and radiation dose delivery.

Procedures

Deceased mice (n = 3) were scanned with an EI XPC micro-CT setup operated under different settings, leading to scan times between 18 h and 13 min. For the shortest scan, the entrance dose was measured with a calibrated PTW 23344 ion chamber. Different data processing methods were applied, retrieving either separate attenuation and phase images, or hybrid (combined attenuation and phase) images. A quantitative comparison was performed based on CNR and spatial resolution measurements for a soft tissue interface.

Results

All phase-based images have led to a higher CNR for the considered soft tissue interface than the attenuation image, independent of scan time. The best relative CNR (a sixfold increase) was observed in one of the hybrid images. Spatial resolution was found to be connected to scan time, with a resolution of approximately 20 μm and 60 μm achieved for the longest and shortest scans, respectively. An entrance dose of approximately 300 mGy was estimated for the scan performed within 13 min.

Conclusions

Despite their preliminary nature, our results suggest that EI XPC bears potential for enhancing the utility of preclinical micro-CT, and, pending further research and development, could ultimately become a valuable technique in this field.

3D-Non-destructive Imaging through Heavy-Metal Eosin Salt Contrast Agents

Conventional histology is a destructive technique based on the evaluation of 2D slices of a 3D biopsy. By using 3D X‐ray histology these obstacles can be overcome, but their application is still restricted due to the inherently low attenuation properties of soft tissue. In order to solve this problem, the tissue can be stained before X‐ray computed tomography imaging (CT) to enhance the soft tissue X‐ray contrast. Evaluation of brominated fluorescein salts revealed a mutual influence of the number of bromine atoms and the cations applied on the achieved contrast enhancement. The dibromo fluorescein barium salt turned out to be the ideal X‐ray contrast agent, allowing for 3D imaging and subsequent complementing counterstaining applying standard histological techniques.

Differentiation of benign and malignant regions in paraffin embedded tissue blocks of pulmonary adenocarcinoma using micro CT scanning of paraffin tissue blocks: a pilot study for method validation

PURPOSE

Micro computed tomography (micro-CT) can provide detailed information about the internal structure of materials. This study aimed to demonstrate the diagnostic value of micro-CT in formalin fixed paraffin embedded pulmonary adenocarcinomas by correlating the micro-CT findings of tumoral and non-tumoral areas with hematoxylin and eosin (HE) sections.

METHODS

Paraffin blocks obtained from three adenocarcinomas were scanned with micro-CT. Ten regions of interest (ROIs) from adenocarcinoma and 11 ROIs from pulmonary parenchyma (ROI-C and ROI-N, respectively) areas were compared regarding the various structural parameters.

RESULTS

All parameters were significantly different regarding the tumoral and non-tumoral ROIs. The percent object volume, structure thickness, structure linear density, connectivity and connectivity density were higher in ROI-Cs (p < 0.000, p < 0.000, p = 0.001, p < 0.000, and p < 0.000 respectively); whereas intersection surface and structure model index were higher in ROI-Ns (p < 0.000 and p < 0.000). The open porosity percentage was higher in ROI-Ns (68.86 + 2.96 vs 48.29 + 5.11, p < 0.000) and the closed porosity percentage was higher in ROI-Cs (2.29 + 0.55 vs 0.57 + 0.17 p < 0.000).

CONCLUSIONS

The tumoral and non-tumoral areas in paraffin blocks can be distinguished from each other, using the quantitative and qualitative information obtained by micro-CT. Making this distinction with quantitative data obtained from micro-CT can therefore be the basis of creating artificial intelligence algorithms in the future.

Challenges and approaches in assessing the interplay between microorganisms and their physical micro-environments

Spatial structure over scales ranging from nanometres to centimetres (and beyond) varies markedly in diverse habitats and the industry-relevant settings that support microbial activity. Developing an understanding of the interplay between a structured environment and the associated microbial processes and ecology is fundamental, but challenging. Several novel approaches have recently been developed and implemented to help address key questions for the field: from the use of imaging tools such as X-ray Computed Tomography to explore microbial growth in soils, to the fabrication of scratched materials to examine microbial-surface interactions, to the design of microfluidic devices to track microbial biofilm formation and the metabolic processes therein. This review discusses new approaches and challenges for incorporating structured elements into the study of microbial processes across different scales. We highlight how such methods can be pivotal for furthering our understanding of microbial interactions with their environments.

Connections between the internal and the external capsules and the globus pallidus in the sheep: A dichromate stain X-ray microtomographic study

Sheep are recognized as useful species for translational neurodegeneration research, in particular for the study of Huntington disease. There is a lack of information regarding the detailed anatomy and connections of the basal ganglia of sheep, in normal myeloarchitectonics and in tract-tracing studies. In this work, the organization of the corticostriatal projections at the level of the putamen and globus pallidus (GP) are explored. For the first time, the myeloarchitectonic pattern of connections between the internal (IC) and the external (EC) capsules with the GP have been investigated in the sheep. Formaldehyde-fixed blocks of the striatum were treated with a metallic stain containing potassium dichromate and visualized using micro-CT (µ-CT). The trivalent chromium (Cr3+), attached to myelin phospholipids, imparts a differential contrast to the grey and white matter compartments, which allows the visualization of myelinated fascicles in µ-CT images. The fascicles were classified according to their topographical location in dorsal supreme fascicles (X, Y, apex) arising from the IC and EC; pre-commissurally, basal fascicles connecting the ventral part of the EC with the lateral zone of the ventral pallidum (VP) and, post-commissurally, superior (Z₁ ), middle (Z₂ ) and lower (Z₃ ) fascicles, connecting at different levels the EC with the GP. The results suggest that the presumptive cortical efferent and afferent fibres to the pallidum could be organized according to a dorsal to ventrolateral topography in the sheep, similar to that seen in other mammals. The proposed methodology has the potential to delineate the myeloarchitectonic patterns of nervous systems and tracts.

Identification of tumor nodule in soft tissue: An inverse finite-element framework based on mechanical characterization

Identification and characterization of nodules in soft tissue, including their size, shape, and location, provide a basis for tumor identification. This study proposes an inverse finite-element (FE) based computational framework, for characterizing the size of examined tissue sample and detecting the presence of embedded tumor nodules using instrumented palpation, without a priori anatomical knowledge. The inverse analysis was applied to a model system, the human prostate, and was based on the reaction forces which can be obtained by trans-rectal mechanical probing and those from an equivalent FE model, which was optimized iteratively, by minimizing an error function between the two cases, toward the target solution. The tumor nodule can be identified through its influence on the stress state of the prostate. The effectiveness of the proposed method was further verified using a realistic prostate model reconstructed from magnetic resonance (MR) images. The results show the proposed framework to be capable of characterizing the key geometrical indices of the prostate and identifying the presence of cancerous nodules. Therefore, it has potential, when combined with instrumented palpation, for primary diagnosis of prostate cancer, and, potentially, solid tumors in other types of soft tissue.

A Recruitment Model of Tendon Viscoelasticity That Incorporates Fibril Creep and Explains Strain-Dependent Relaxation

Soft tissues exhibit complex viscoelastic behavior, including strain-rate dependence, hysteresis, and strain-dependent relaxation. In this paper, a model for soft tissue viscoelasticity is developed that captures all of these features and is based upon collagen recruitment, whereby fibrils contribute to tissue stiffness only when taut. We build upon existing recruitment models by additionally accounting for fibril creep and by explicitly modeling the contribution of the matrix to the overall tissue viscoelasticity. The fibrils and matrix are modeled as linear viscoelastic and each fibril has an associated critical strain (corresponding to its length) at which it becomes taut. The model is used to fit relaxation tests on three rat tail tendon fascicles and predict their response to cyclic loading. It is shown that all of these mechanical tests can be reproduced accurately with a single set of constitutive parameters, the only difference between each fascicle being the distribution of their fibril crimp lengths. By accounting for fibril creep, we are able to predict how the fibril length distribution of a fascicle changes over time under a given deformation. Furthermore, the phenomenon of strain-dependent relaxation is explained as arising from the competition between the fibril and matrix relaxation functions.

X-ray Micro-Computed Tomography: An Emerging Technology to Analyze Vascular Calcification in Animal Models

Vascular calcification describes the formation of mineralized tissue within the blood vessel wall, and it is highly associated with increased cardiovascular morbidity and mortality in patients with chronic kidney disease, diabetes, and atherosclerosis. In this article, we briefly review different rodent models used to study vascular calcification in vivo, and critically assess the strengths and weaknesses of the current techniques used to analyze and quantify calcification in these models, namely 2-D histology and the o-cresolphthalein assay. In light of this, we examine X-ray micro-computed tomography (µCT) as an emerging complementary tool for the analysis of vascular calcification in animal models. We demonstrate that this non-destructive technique allows us to simultaneously quantify and localize calcification in an intact vessel in 3-D, and we consider recent advances in µCT sample preparation techniques. This review also discusses the potential to combine 3-D µCT analyses with subsequent 2-D histological, immunohistochemical, and proteomic approaches in correlative microscopy workflows to obtain rich, multifaceted information on calcification volume, calcification load, and signaling mechanisms from within the same arterial segment. In conclusion we briefly discuss the potential use of µCT to visualize and measure vascular calcification in vivo in real-time.

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.

X-ray computed tomography in life sciences

Recent developments within micro-computed tomography (μCT) imaging have combined to extend our capacity to image tissue in three (3D) and four (4D) dimensions at micron and sub-micron spatial resolutions, opening the way for virtual histology, live cell imaging, subcellular imaging and correlative microscopy. Pivotal to this has been the development of methods to extend the contrast achievable for soft tissue. Herein, we review the new capabilities within the field of life sciences imaging, and consider how future developments in this field could further benefit the life sciences community.

X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes)

In 2016, the type-material of ten of the 15 Brazilian land planarians (Platyhelminthes, Tricladida, Geoplanidae) described by Schirch (1929) was discovered deposited in the Museu Nacional do Rio de Janeiro (MNRJ). Schirch only described the external morphology of these species, all originally placed in the genus Geoplana. By the 1930s and 1950s Geoplanaitatiayana, G.plana, and G.rezendei underwent taxonomic revision based on the study of non-type specimens. The remaining 12 species also underwent a taxonomic revision but only based on the literature. Current names of these species are Geoplanagoettei, Pseudogeoplanaarpi, Ps.blaseri, Ps.bonita, Ps.bresslaui, Ps.cardosi, Ps.doederleini, Ps.lumbricoides, Ps.obscura, Ps.riedeli, Ps.theresopolitana, and Ps.wetzeli. The species Geoplanamaximiliani sensu Schirch (1929) was renamed as Ps.schirchi Ogren & Kawakatsu, 1990.

The present study reports a taxonomic revision of seven of Schirch’s species using type material, namely Obamaitatiayana, Pasiphaplana, Pseudogeoplanaarpi, Ps.bresslaui, Ps.doederleini, Ps.schirchi and Ps.wetzeli. Additional specimens of some of these species were also examined. Morphological data from histological preparations and from virtual sections were obtained through a non-destructive technique of X-ray computed microtomography (µCT). This approach resulted in the preservation of the entire body of at least one type-specimen of each species, and the holotype of Ps.bresslaui. Conspecificity of O.itatiayana and P.plana was confirmed, as previously reported in the literature. It is also proposed that Ps.bresslaui belongs to the genus Paraba, while the other species should remain in Pseudogeoplana, since type-specimens are either immature, poorly preserved or simply lost.

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.

3D vessel-wall virtual histology of whole-body perfused mice using a novel heavy element stain

Virtual histology – utilizing high-resolution three-dimensional imaging – is becoming readily available. Micro-computed tomography (micro-CT) is widely available and is often coupled with x-ray attenuating histological stains that mark specific tissue components for 3D virtual histology. In this study we describe a new tri-element x-ray attenuating stain and perfusion protocol that provides micro-CT contrast of the entire vasculature of an intact mouse. The stain – derived from an established histology stain (Verhoeff’s) – is modified to enable perfusion through the vasculature; the attenuating elements of the stain are iodine, aluminum, and iron. After a 30-minute perfusion through the vasculature (10-minute flushing with detergent-containing saline followed by 15-minute perfusion with the stain and a final 5-minute saline flush), animals are scanned using micro-CT. We demonstrate that the new staining protocol enables sharp delineation of the vessel walls in three dimensions over the whole body; corresponding histological analysis verified that the CT stain is localized primarily in the endothelial cells and media of large arteries and the endothelium of smaller vessels, such as the coronaries. The rapid perfusion and scanning protocol ensured that all tissues are available for further analysis via higher resolution CT of smaller sections or traditional histological sectioning.

MicroCT imaging reveals differential 3D micro-scale remodelling of the murine aorta in ageing and Marfan syndrome

Aortic wall remodelling is a key feature of both ageing and genetic connective tissue diseases, which are associated with vasculopathies such as Marfan syndrome (MFS). Although the aorta is a 3D structure, little attention has been paid to volumetric assessment, primarily due to the limitations of conventional imaging techniques. Phase-contrast microCT is an emerging imaging technique, which is able to resolve the 3D micro-scale structure of large samples without the need for staining or sectioning.

Methods: Here, we have used synchrotron-based phase-contrast microCT to image aortae of wild type (WT) and MFS Fbn1^C1039G/+ mice aged 3, 6 and 9 months old (n=5). We have also developed a new computational approach to automatically measure key histological parameters.

Results: This analysis revealed that WT mice undergo age-dependent aortic remodelling characterised by increases in ascending aorta diameter, tunica media thickness and cross-sectional area. The MFS aortic wall was subject to comparable remodelling, but the magnitudes of the changes were significantly exacerbated, particularly in 9 month-old MFS mice with ascending aorta wall dilations. Moreover, this morphological remodelling in MFS aorta included internal elastic lamina surface breaks that extended throughout the MFS ascending aorta and were already evident in animals who had not yet developed aneurysms.

Conclusions: Our 3D microCT study of the sub-micron wall structure of whole, intact aorta reveals that histological remodelling of the tunica media in MFS could be viewed as an accelerated ageing process, and that phase-contrast microCT combined with computational image analysis allows the visualisation and quantification of 3D morphological remodelling in large volumes of unstained vascular tissues.

Four-Dimensional Imaging of Soft Tissue and Implanted Biomaterial Mechanics: A Barbed Suture Case Study for Tendon Repair

Timely, recent developments in X-ray microcomputed tomography (XμCT) imaging such as increased resolution and improved sample preparation enable nondestructive time-lapse imaging of polymeric biomaterials when implanted in soft tissue, which we demonstrate herein. Imaging the full three-dimensional (3D) structure of an implanted biomaterial provides new opportunities to assess the micromechanics of the interface between the implant and tissues and how this changes over time as force is applied in load-bearing musculoskeletal applications. In this paper, we present a case study demonstrating in situ XμCT and finite element analysis, using a dynamically loaded barbed suture repair for its novel use in tendon tissue. The aim of this study was to identify the distribution of stress in the suture and tendon as load is applied. The data gained demonstrate a clear 3D visualization of microscale features in both the tissue and implant in wet conditions. XμCT imaging has revealed, for the first time, pores around the suture, preventing full engagement of all the barbs with the tendon tissue. Subsequent finite element analysis reveals the localized stress and strain, which are not evenly distributed along the suture, or throughout the tissue. This case study demonstrates for the first time a powerful in situ mechanical imaging tool, which could be readily adapted by other laboratories to interrogate and optimize the interface between the implanted biomaterials and the soft tissue.

3D multiscale imaging of human vocal folds using synchrotron X-ray microtomography in phase retrieval mode

Human vocal folds possess outstanding abilities to endure large, reversible deformations and to vibrate up to more than thousand cycles per second. This unique performance mainly results from their complex specific 3D and multiscale structure, which is very difficult to investigate experimentally and still presents challenges using either confocal microscopy, MRI or X-ray microtomography in absorption mode. To circumvent these difficulties, we used high-resolution synchrotron X-ray microtomography with phase retrieval and report the first ex vivo 3D images of human vocal-fold tissues at multiple scales. Various relevant descriptors of structure were extracted from the images: geometry of vocal folds at rest or in a stretched phonatory-like position, shape and size of their layered fibrous architectures, orientation, shape and size of the muscle fibres as well as the set of collagen and elastin fibre bundles constituting these layers. The developed methodology opens a promising insight into voice biomechanics, which will allow further assessment of the micromechanics of the vocal folds and their vibratory properties. This will then provide valuable guidelines for the design of new mimetic biomaterials for the next generation of artificial larynges.

X-ray micro computed-tomography

Emily Baird and Gavin Taylor describe how you can make three-dimensional models of biological samples using x-ray micro-computed tomography.

A review of techniques for visualising soft tissue microstructure deformation and quantifying strain Ex Vivo

Many biological tissues have a complex hierarchical structure allowing them to function under demanding physiological loading conditions. Structural changes caused by ageing or disease can lead to loss of mechanical function. Therefore, it is necessary to characterise tissue structure to understand normal tissue function and the progression of disease. Ideally intact native tissues should be imaged in 3D and under physiological loading conditions. The current published in situ imaging methodologies demonstrate a compromise between imaging limitations and maintaining the samples native mechanical function. This review gives an overview of in situ imaging techniques used to visualise microstructural deformation of soft tissue, including three case studies of different tissues (tendon, intervertebral disc and artery). Some of the imaging techniques restricted analysis to observational mechanics or discrete strain measurement from invasive markers. Full-field local surface strain measurement has been achieved using digital image correlation. Volumetric strain fields have successfully been quantified from in situ X-ray microtomography (micro-CT) studies of bone using digital volume correlation but not in soft tissue due to low X-ray transmission contrast. With the latest developments in micro-CT showing in-line phase contrast capability to resolve native soft tissue microstructure, there is potential for future soft tissue mechanics research where 3D local strain can be quantified. These methods will provide information on the local 3D micromechanical environment experienced by cells in healthy, aged and diseased tissues. It is hoped that future applications of in situ imaging techniques will impact positively on the design and testing of potential tissue replacements or regenerative therapies. LAY DESCRIPTION: The soft tissues in our bodies, such as tendons, intervertebral discs and arteries, have evolved to have complicated structures which deform and bear load during normal function. Small changes in these structures can occur with age and disease which then leads to loss of function. Therefore, it is important to image tissue microstructure in 3D and under functional conditions. This paper gives an overview of imaging techniques used to record the deformation of soft tissue microstructures. Commonly there are compromises between obtaining the best imaging result and retaining the samples native structure and function. For example, invasive markers and dissecting samples damages the tissues natural structure, and staining or clearing (making the tissue more transparent) can distort tissue structure. Structural deformation has been quantified from 2D imaging techniques (digital image correlation) to create surface strain maps which help identify local tissue mechanics. When extended to 3D (digital volume correlation), deformation measurement has been limited to bone samples using X-ray micro-CT. Recently it has been possible to image the 3D structure of soft tissue using X-ray micro-CT meaning that there is potential for internal soft tissue mechanics to be mapped in 3D. Future application of micro-CT and digital volume correlation will be important for soft tissue mechanics studies particularly to understand normal function, progression of disease and in the design of tissue replacements.

The Calamistrum of the Feather-Legged Spider Uloborus plumipes Investigated by Focused Ion Beam and Scanning Electron Microscopy (FIB-SEM) Tomography

Spiders are natural specialists in fiber processing. In particular, cribellate spiders manifest this ability as they produce a wool of nanofibers to capture prey. During its production they deploy a sophisticated movement of their spinnerets to darn in the fibers as well as a comb-like row of setae, termed calamistrum, on the metatarsus which plays a key role in nanofiber processing. In comparison to the elaborate nanofiber extraction and handling process by the spider's calamistrum, the human endeavors of spinning and handling of artificial nanofibers is still a primitive technical process. An implementation of biomimetics in spinning technology could lead to new materials and applications. Despite the general progress in related fields of nanoscience, the expected leap forward in spinning technology depends on a better understanding of the specific shapes and surfaces that control the forces at the nanoscale and that are involved in the mechanical processing of the nanofibers, respectively. In this study, the authors investigated the morphology of the calamistrum of the cribellate spider Uloborus plumipes. Focused ion beam and scanning electron microscopy tomography provided a good image contrast and the best trade-off between investigation volume and spatial resolution. A comprehensive three-dimensional model is presented and the putative role of the calamistrum in nanofiber processing is discussed.

Multi-scale X-ray computed tomography to detect and localize metal-based nanomaterials in lung tissues of in vivo exposed mice

In this methodological study, we demonstrated the relevance of 3D imaging performed at various scales for the ex vivo detection and location of cerium oxide nanomaterials (CeO₂-NMs) in mouse lung. X-ray micro-computed tomography (micro-CT) with a voxel size from 14 µm to 1 µm (micro-CT) was combined with X-ray nano-computed tomography with a voxel size of 63 nm (nano-CT). An optimized protocol was proposed to facilitate the sample preparation, to minimize the experimental artifacts and to optimize the contrast of soft tissues exposed to metal-based nanomaterials (NMs). 3D imaging of the NMs biodistribution in lung tissues was consolidated by combining a vast variety of techniques in a correlative approach: histological observations, 2D chemical mapping and speciation analysis were performed for an unambiguous detection of NMs. This original methodological approach was developed following a worst-case scenario of exposure, i.e. high dose of exposure with administration via intra-tracheal instillation. Results highlighted both (i) the non-uniform distribution of CeO₂-NMs within the entire lung lobe (using large field-of-view micro-CT) and (ii) the detection of CeO₂-NMs down to the individual cell scale, e.g. macrophage scale (using nano-CT with a voxel size of 63 nm).

Reciprocal Spatiotemporally Controlled Apoptosis Regulates Wolffian Duct Cloaca Fusion

The epithelial Wolffian duct (WD) inserts into the cloaca (primitive bladder) before metanephric kidney development, thereby establishing the initial plumbing for eventual joining of the ureters and bladder. Defects in this process cause common anomalies in the spectrum of congenital anomalies of the kidney and urinary tract (CAKUT). However, developmental, cellular, and molecular mechanisms of WD-cloaca fusion are poorly understood. Through systematic analysis of early WD tip development in mice, we discovered that a novel process of spatiotemporally regulated apoptosis in WD and cloaca was necessary for WD-cloaca fusion. Aberrant RET tyrosine kinase signaling through tyrosine (Y) 1062, to which PI3K- or ERK-activating proteins dock, or Y1015, to which PLCγ docks, has been shown to cause CAKUT-like defects. Cloacal apoptosis did not occur in RetY1062F mutants, in which WDs did not reach the cloaca, or in RetY1015F mutants, in which WD tips reached the cloaca but did not fuse. Moreover, inhibition of ERK or apoptosis prevented WD-cloaca fusion in cultures, and WD-specific genetic deletion of YAP attenuated cloacal apoptosis and WD-cloacal fusion in vivo Thus, cloacal apoptosis requires direct contact and signals from the WD tip and is necessary for WD-cloacal fusion. These findings may explain the mechanisms of many CAKUT.

Novel Application of Micro-Computerized Tomography for Morphologic Characterization of the Murine Penis

BACKGROUND

The murine penis model has enriched our understanding of anomalous penile development. The morphologic characterization of the murine penis using conventional serial sectioning methods is labor intensive and prone to errors.

AIM

To develop a novel application of micro-computerized tomography (micro-CT) with iodine staining for rapid, non-destructive morphologic study of murine penis structure.

METHODS

Penises were dissected from 10 adult wild-type mice and imaged using micro-CT with iodine staining. Images were acquired at 5-μm spatial resolution on a Bruker SkyScan 1272 micro-CT system. After images were acquired, the specimens were washed of any remaining iodine and embedded in paraffin for conventional histologic examination. Histologic and micro-CT measurements for all specimens were made by 2 independent observers.

OUTCOMES

Measurements of penile structures were made on virtual micro-CT sections and histologic slides.

RESULTS

The Lin concordance correlation coefficient demonstrated almost perfect strength of agreement for interobserver variability for histologic section (0.9995, 95% CI = 0.9990-0.9997) and micro-CT section (0.9982, 95% CI = 0.9963-0.9991) measurements. Bland-Altman analysis for agreement between the 2 modalities of measurement demonstrated mean differences of -0.029, 0.022, and -0.068 mm for male urogenital mating protuberance, baculum, and penile glans length, respectively. There did not appear to be a bias for overestimation or underestimation of measured lengths and limits of agreement were narrow.

CLINICAL TRANSLATION

The enhanced ability offered by micro-CT to phenotype the murine penis has the potential to improve translational studies examining the molecular pathways contributing to anomalous penile development.

STRENGTHS AND LIMITATIONS

The present study describes the first reported use of micro-CT with iodine staining for imaging the murine penis. Producing repeated histologic sections of identical orientation was limited by inherent imperfections in mounting and tissue sectioning, but this was compensated for by using micro-CT reconstructions to identify matching virtual sections.

CONCLUSION

This study demonstrates the successful use of micro-CT with iodine staining, which has the potential for submicron spatial resolution, as a non-destructive method of characterizing murine penile morphology. O'Neill M, Huang GO, Lamb DJ. Novel Application of Micro-Computerized Tomography for Morphologic Characterization of the Murine Penis. J Sex Med 2017;14:1533-1539.

* Microcomputed Tomography Technique for In Vivo Three-Dimensional Fat Tissue Volume Evaluation After Polymer Injection

Tissue engineering technologies are new and promising techniques in fat tissue reconstruction. However, to assess their efficacy before any clinical application, in vivo experiments are mandatory. This study assesses whether microcomputed tomography (CT) scan imaging is suitable to analyze in vivo the behavior of injected engineered polymer and changes in fat tissue. The volume of mice inguinal fat pads and the resorption rate of different polymers were analyzed by CT scan for up to 3 months. Different biomaterials were used, including our innovative microspheres loaded with oleic acid. We were able to follow in vivo the polymer and the fat volume of the same animals during a long-term follow-up of 90 days. Semiautomatic three-dimensional quantification allowed to determine the fat volume enhancement after injection, as well as the resorption rate of our product compared to other biomaterials (i.e., polylactic and hyaluronic acid) until 90 days. Our results demonstrate the encouraging proof-of-principle evidence for the application of micro-CT scan technology to follow in vivo biodegradable polymers in a fat tissue engineering approach. This noninvasive technique offers the advantages of the long-term follow-up of fat tissue and synthetic materials in the same animals, which allows both a scientific evaluation of the measurements and the reduction of the number of animals used in in vivo protocols in accordance with the 3 "R" principles governing the use of animals in science.

The relative compliance of energy-storing tendons may be due to the helical fibril arrangement of their fascicles

A nonlinear elastic microstructural model is used to investigate the relationship between structure and function in energy-storing and positional tendons. The model is used to fit mechanical tension test data from the equine common digital extensor tendon (CDET) and superficial digital flexor tendon (SDFT), which are used as archetypes of positional and energy-storing tendons, respectively. The fibril crimp and fascicle helix angles of the two tendon types are used as fitting parameters in the mathematical model to predict their values. The outer fibril crimp angles were predicted to be 15.1° ± 2.3° in the CDET and 15.8° ± 4.1° in the SDFT, and the average crimp angles were predicted to be 10.0° ± 1.5° in the CDET and 10.5° ± 2.7° in the SDFT. The crimp angles were not found to be statistically significantly different between the two tendon types (p = 0.572). By contrast, the fascicle helix angles were predicted to be 7.9° ± 9.3° in the CDET and 29.1° ± 10.3° in the SDFT and were found to be statistically highly significantly different between the two tendon types (p < 0.001). This supports previous qualitative observations that helical substructures are more likely to be found in energy-storing tendons than in positional tendons and suggests that the relative compliance of energy-storing tendons may be directly caused by these helical substructures.

Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods

Background

High-resolution 3D imaging of intact tissue facilitates cellular and subcellular analyses of complex structures within their native environment. However, difficulties associated with immunolabelling and imaging fluorescent proteins deep within whole organs have restricted their applications to thin sections or processed tissue preparations, precluding comprehensive and rapid 3D visualisation. Several tissue clearing methods have been established to circumvent issues associated with depth of imaging in opaque specimens. The application of these techniques to study the elaborate architecture of the mouse mammary gland has yet to be investigated.

Methods

Multiple tissue clearing methods were applied to intact virgin and lactating mammary glands, namely 3D imaging of solvent-cleared organs, see deep brain (seeDB), clear unobstructed brain imaging cocktails (CUBIC) and passive clarity technique. Using confocal, two-photon and light sheet microscopy, their compatibility with whole-mount immunofluorescent labelling and 3D imaging of mammary tissue was examined. In addition, their suitability for the analysis of mouse mammary tumours was also assessed.

Results

Varying degrees of optical transparency, tissue preservation and fluorescent signal conservation were observed between the different clearing methods. SeeDB and CUBIC protocols were considered superior for volumetric fluorescence imaging and whole-mount histochemical staining, respectively. Techniques were compatible with 3D imaging on a variety of platforms, enabling visualisation of mammary ductal and lobulo-alveolar structures at vastly improved depths in cleared tissue.

Conclusions

The utility of whole-organ tissue clearing protocols was assessed in the mouse mammary gland. Most methods utilised affordable and widely available reagents, and were compatible with standard confocal microscopy. These techniques enable high-resolution, 3D imaging and phenotyping of mammary cells and tumours in situ, and will significantly enhance our understanding of both normal and pathological mammary gland development.

Electronic supplementary material

The online version of this article (doi:10.1186/s13058-016-0754-9) contains supplementary material, which is available to authorized users.