Extending two-dimensional histology into the third dimension through conventional micro computed tomography.

Histological examination achieves sub-micrometer resolution laterally. In the third dimension, however, resolution is limited to section thickness. In addition, histological sectioning and mounting sections on glass slides introduce tissue-dependent stress and strain. In contrast, state-of-the-art hard X-ray micro computed tomography (µCT) systems provide isotropic sub-micrometer resolution and avoid sectioning artefacts. The drawback of µCT in the absorption contrast mode for visualising physically soft tissue is a low attenuation difference between anatomical features. In this communication, we demonstrate that formalin-fixed paraffin-embedded human cerebellum yields appropriate absorption contrast in laboratory-based µCT data, comparable to conventional histological sections. Purkinje cells, for example, are readily visible. In order to investigate the pros and cons of complementary approaches, two- and three-dimensional data were manually and automatically registered. The joint histogram of histology and the related µCT slice allows for a detailed discussion on how to integrate two-dimensional information from histology into a three-dimensional tomography dataset. This methodology is not only rewarding for the analysis of the human cerebellum, but it also has relevance for investigations of tissue biopsies and post-mortem applications. Our data indicate that laboratory-based µCT as a modality can fill the gap between synchrotron radiation-based µCT and histology for a variety of tissues. As the information from haematoxylin and eosin (H&E) stained sections and µCT data is related, one can colourise local X-ray absorption values according to the H&E stain. Hence, µCT data can correlate and virtually extend two-dimensional (2D) histology data into the third dimension.

Terabyte-scale supervised 3D training and benchmarking dataset of the mouse kidney.

The performance of machine learning algorithms, when used for segmenting 3D biomedical images, does not reach the level expected based on results achieved with 2D photos. This may be explained by the comparative lack of high-volume, high-quality training datasets, which require state-of-the-art imaging facilities, domain experts for annotation and large computational and personal resources. The HR-Kidney dataset presented in this work bridges this gap by providing 1.7 TB of artefact-corrected synchrotron radiation-based X-ray phase-contrast microtomography images of whole mouse kidneys and validated segmentations of 33 729 glomeruli, which corresponds to a one to two orders of magnitude increase over currently available biomedical datasets. The image sets also contain the underlying raw data, threshold- and morphology-based semi-automatic segmentations of renal vasculature and uriniferous tubules, as well as true 3D manual annotations. We therewith provide a broad basis for the scientific community to build upon and expand in the fields of image processing, data augmentation and machine learning, in particular unsupervised and semi-supervised learning investigations, as well as transfer learning and generative adversarial networks.

Three-dimensional quantification of capillary networks in healthy and cancerous tissues of two mice.

A key issue in developing strategies against diseases such as cancer is the analysis of the vessel tree in comparison to the healthy one. In the search for parameters that might be characteristic for tumor capillaries we study the vascularization in mice for cancerous and healthy tissues using synchrotron radiation-based micro computed tomography in absorption and phase contrast modes. Our investigations are based on absorption tomograms of casted healthy and cancerous tissues as well as a phase tomogram of a fixated tumor. We demonstrate how the voxel-based tomography data can be vectorized to assess the capillary networks quantitatively. The processing includes segmentation, skeletonization, and vectorization to finally extract the vessel parameters. The mean diameter of capillaries in healthy and cancerous tissues corresponds to (8.0±1.1) µm and (3.9±1.1) µm, respectively. Further evaluated parameters show marginal or no differences between capillaries in healthy and cancerous tissues, namely fractal dimension 2.3±0.3 vs. 2.3±0.2, tortuosity (SOAM) 0.18 rad/µm vs. 0.24 rad/µm and vessel length 20 µm vs. 17 µm. The bifurcation angles exhibit a narrow distribution around 115°. Furthermore, we show that phase tomography is a powerful alternative to absorption tomography of casts for the vessel visualization omitting any invasive specimen preparation procedure.

Ex vivo evaluation of an atherosclerotic human coronary artery via histology and high-resolution hard X-ray tomography.

Atherosclerotic arteries exhibit characteristic constrictions and substantial deviations from cylindrical shape. Therefore, determining the artery's cross-section along the centerline is challenging, although high-resolution isotropic three-dimensional data are available. Herein, we apply high-resolution computed tomography in absorption and phase to a plaque-containing human artery post-mortem, through the course of the preparation stages for histology. We identify the impact of paraffin embedding and decalcification on the artery lumen. For automatic extraction of lumen's cross-section along centerline we present a dedicated pipeline. Comparing fixated tissue before and after paraffin embedding gives rise to shape changes with lumen reduction to 50-80%. The histological slicing induces further deformations with respect to tomography. Data acquired after decalcification show debris unintentionally distributed within the vessel preventing the reliable automatic lumen segmentation. Comparing tomography of laboratory- and synchrotron-radiation-based X rays by means of joint histogram analysis leads us to conclude that advanced desktop tomography is capable of quantifying the artery's lumen as an essential input for blood flow simulations. The results indicate that the most reliable lumen quantification is achieved by imaging the non-decalcified specimen fixed in formalin, using phase contrast modality and a dedicated processing pipeline. This study focusses on a methodology to quantitatively evaluate diseased artery segments post-mortem and provides unique structural parameters on the treatment-induced local shrinkage, which will be the basis of future studies on the flow in vessels affected by constrictions.

Three-dimensional and non-destructive characterization of nerves inside conduits using laboratory-based micro computed tomography.

BACKGROUND: Histological assessment of peripheral nerve regeneration in animals is tedious, time-consuming and challenging for three-dimensional analysis. NEW METHOD: The present study reports on how and to what extent micro computed tomography of paraffin-embedded samples can provide a reliable three-dimensional approach for quantitative analysis of peripheral nerves. RESULTS: Rat sciatic nerves were harvested, formalin-fixated, positioned into nerve conduits (NC), paraffin-embedded, and imaged using a laboratory-based X-ray microtomography system with an isotropic voxel length of 4µm. Suitable quantitative measures were identified and automatically evaluated, i.e. nerve length, cross-sectional area and volume, as well as vascular structures, to be used as an assessment and comparison indicator of regeneration quality. COMPARISON WITH EXISTING METHODS: Compared to imaging using contrast agents, the investigated specimens can subsequently undergo the conventional histological analysis without requiring additional preparation steps. Contrast and spatial resolution are also increased significantly. CONCLUSIONS: We demonstrate the potential of the micro computed tomography for non-destructive monitoring of peripheral nerves inside the conduits.

Three-dimensional imaging and analysis of entire peripheral nerves after repair and reconstruction.

BACKGROUND: We wanted to achieve a three-dimensional (3D), non-destructive imaging and automatic post-analysis and evaluation of reconstructed peripheral nerves without involving cutting and staining processes. NEW METHOD: We used a laboratory-based micro computed tomography system for imaging, as well as a custom analysis protocol. The sample preparation was also adapted in order to achieve 3D images with true micrometer resolution and suitable contrast. RESULTS: Analysis of the acquired tomograms enabled the quantitative assessment of 3D tissue structures, i.e., surface morphology, nerve fascicles, nerve tissue volume, geometry, and vascular regrowth. The resulting data showed significant differences between operated animals and non-operated controls. COMPARISON WITH EXISTING METHODS: Our approach avoids the sampling error associated with conventional 2D visualization approaches and holds promise for automation of the analysis of large series of datasets. CONCLUSIONS: We have presented a potential way for 3D imaging and analysis of entire regenerated nerves non-destructively, paving the way for high-throughput analysis of therapeutic conditions of treating adult nerve injuries.

Hard X-Ray Nanoholotomography: Large-Scale, Label-Free, 3D Neuroimaging beyond Optical Limit.

There have been great efforts on the nanoscale 3D probing of brain tissues to image subcellular morphologies. However, limitations in terms of tissue coverage, anisotropic resolution, stain dependence, and complex sample preparation all hinder achieving a better understanding of the human brain functioning in the subcellular context. Herein, X-ray nanoholotomography is introduced as an emerging synchrotron radiation-based technology for large-scale, label-free, direct imaging with isotropic voxel sizes down to 25 nm, exhibiting a spatial resolution down to 88 nm. The procedure is nondestructive as it does not require physical slicing. Hence, it allows subsequent imaging by complementary techniques, including histology. The feasibility of this 3D imaging approach is demonstrated on human cerebellum and neocortex specimens derived from paraffin-embedded tissue blocks. The obtained results are compared to hematoxylin and eosin stained histological sections and showcase the ability for rapid hierarchical neuroimaging and automatic rebuilding of the neuronal architecture at the level of a single cell nucleolus. The findings indicate that nanoholotomography can complement microscopy not only by large isotropic volumetric data but also by morphological details on the sub-100 nm level, addressing many of the present challenges in brain tissue characterization and probably becoming an important tool in nanoanatomy.

Tomographic brain imaging with nucleolar detail and automatic cell counting.

Brain tissue evaluation is essential for gaining in-depth insight into its diseases and disorders. Imaging the human brain in three dimensions has always been a challenge on the cell level. In vivo methods lack spatial resolution, and optical microscopy has a limited penetration depth. Herein, we show that hard X-ray phase tomography can visualise a volume of up to 43 mm(3) of human post mortem or biopsy brain samples, by demonstrating the method on the cerebellum. We automatically identified 5,000 Purkinje cells with an error of less than 5% at their layer and determined the local surface density to 165 cells per mm(2) on average. Moreover, we highlight that three-dimensional data allows for the segmentation of sub-cellular structures, including dendritic tree and Purkinje cell nucleoli, without dedicated staining. The method suggests that automatic cell feature quantification of human tissues is feasible in phase tomograms obtained with isotropic resolution in a label-free manner.

Artificial Muscle Devices: Innovations and Prospects for Fecal Incontinence Treatment.

Fecal incontinence describes the involuntary loss of bowel content, which is responsible for stigmatization and social exclusion. It affects about 45% of retirement home residents and overall more than 12% of the adult population. Severe fecal incontinence can be treated by the implantation of an artificial sphincter. Currently available implants, however, are not part of everyday surgery due to long-term re-operation rates of 95% and definitive explantation rates of 40%. Such figures suggest that the implants fail to reproduce the capabilities of the natural sphincter. This article reviews the artificial sphincters on the market and under development, presents their physical principles of operation and critically analyzes their performance. We highlight the geometrical and mechanical parameters crucial for the design of an artificial fecal sphincter and propose more advanced mechanisms of action for a biomimetic device with sensory feedback. Dielectric electro-active polymer actuators are especially attractive because of their versatility, response time, reaction forces, and energy consumption. The availability of such technology will enable fast pressure adaption comparable to the natural feedback mechanism, so that tissue atrophy and erosion can be avoided while maintaining continence during daily activities.

Remeshed smoothed particle hydrodynamics simulation of the mechanical behavior of human organs.

In computer aided surgery the accurate simulation of the mechanical behavior of human organs is essential for the development of surgical simulators. In this paper we introduce particle based simulations of two different human organ materials modeled as linear viscoelastic solids. The constitutive equations for the material behavior are discretized using a particle approach based on the Smoothed Particle Hydrodynamics (SPH) method while the body surface is tracked using level sets. A key aspect of this approach is its flexibility which allows the simulation of complex time varying topologies with large deformations. The accuracy of the original formulation is significantly enhanced by using a particle reinitialization technique resulting in remeshed Smoothed Particle Hydrodynamics (rSPH). The mechanical parameters of the systems used in the simulations are derived from experimental measurements on human cadaver organs. We compare the mechanical behavior of liver- and kidney-like materials based on the dynamic simulations of a tensile test case. Moreover, we present a particle based reconstruction of the liver topology and its strain distribution under a small local load. Finally, we demonstrate a unified formulation of fluid structure interaction based on particle methods.