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Purpose: Histology is the gold standard for sub-cellular visualization of the mouse brain. It offers excellent in-plane resolution, but a comparably low out-of-plane resolution due to physical sectioning. X-ray microtomography does not require this trade-off. Tomographic imaging of the entire mouse brain with isotropic cellular resolution produces datasets of multiple terabytes in size. These data must be processed and made accessible to domain experts who may have only limited image processing knowledge. Approach: Extended-field X-ray microtomography covering an entire mouse brain was performed. The 4,495 projections from 8 $\times$ 8 offset acquisitions were stitched to reconstruct a volume of 15,000$^3$ voxels. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs. Results: We present a 3.3 teravoxel dataset covering a full mouse brain with 0.65 $\mu$m voxel size. The data were blockwise transformed to a common coordinate system, then stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer. Conclusions: This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The data are publicly available and easily accessible for domain experts via browser-based viewers., Comment: 21 pages, 9 figures, submitted to journal

The effectiveness of a series of optically transparent aligners for orthodontic treatments depends on the anchoring of each tooth. In contrast with roots, the crowns' positions and orientations are measurable with intraoral scans, thus avoiding any X-ray dose. Exemplified by two patients, we demonstrate that three-dimensional crown movements could be determined with micrometer precision by registering weekly intraoral scans. The data show the movement and orientation changes of the individual crowns of the upper and lower jaws as the result of the forces generated by the series of aligners. During the first weeks, the canines and incisors were more affected than the premolars and molars. We detected an overall tooth movement of up to about 1 mm during a nine-week treatment. The data on these orthodontic treatments indicate the extent to which actual tooth movement lags behind the treatment plan as represented by the aligner shapes. The proposed procedure can not only be used to quantify the clinical outcome of the therapy, but also to improve future planning of orthodontic treatments for each specific patient. The study should be treated with caution because only two cases have been investigated and the approach should be applied to a reasonably large cohort to reach strong conclusions regarding efficiency and efficacy of the therapeutic approach., Comment: 18 pages, 9 figures, accepted by MDPI journal Oral

Imaging of microvasculature is primarily performed with X-ray contrast agents, owing to the wide availability of absorption-contrast laboratory source microCT compared to phase contrast capable devices. Standard commercial contrast agents used in angiography are not suitable for high-resolution imaging ex vivo, however, as they are small molecular compounds capable of diffusing through blood vessel walls within minutes. Large nanoparticle-based blood pool contrast agents on the other hand exhibit problems with aggregation, resulting in clogging in the smallest blood vessels. Injection with solidifying plastic resins has, therefore, remained the gold standard for microvascular imaging, despite the considerable amount of training and optimization needed to properly perfuse the viscous compounds. Even with optimization, frequent gas and water inclusions commonly result in interrupted vessel segments. This lack of suitable compounds has led us to develop the polymeric, cross-linkable X-ray contrast agent XlinCA. As a water-soluble organic molecule, aggregation and inclusions are inherently avoided. High molecular weight allows it to be retained even in the highly fenestrated vasculature of the kidney filtration system. It can be covalently crosslinked using the same aldehydes used in tissue fixation protocols, leading to stable and permanent contrast. These properties allowed us to image whole mice and individual organs in 6 to 12-month-old C57BL/6J mice without requiring lengthy optimizations of injection rates and pressures, while at the same time achieving greatly improved filling of the vasculature compared to resin-based vascular casting. This work aims at illuminating the rationales, processes and challenges involved in creating this recently developed contrast agent., Comment: 10 pages, 6 figures

Joint tissues consist of trabecular and cortical bone as well as calcified and hyaline cartilage, which presents a challenge for hard X-ray-based visualization on the sub-cellular level due to the wide range of local X-ray absorption values. The density of the calcified tissues requires rather high photon energy, which often leads to insufficient contrast within the cartilage and impedes the visualization of individual biological cells. Decalcification of the tissues reduces the total and local X-ray absorption values and allows for selecting a lower photon energy. Further contrast enhancement can be achieved by ethanol fixation and paraffin tissue embedding. In this study, we (i) searched for an appropriate visualization method to investigate lesions generated by a laser osteotome and (ii) visualized a decalcified porcine joint after ethanol fixation and subsequent paraffin embedding using laboratory- and synchrotron radiation-based microtomography. The experiments at the ANATOMIX beamline of Synchrotron SOLEIL were performed in off-axis scan mode with a pixel size of 1.3 um. Individual cells in all layers of the joint could be made visible and the effect of ethanol fixation and paraffin embedding demonstrated., Comment: 10 pages. Event: SPIE Optical Engineering + Applications, 2022, San Diego, California, United States

The growth of plants, animals, and humans can give rise to layered structures associated with annual periodicity. Thickness variations are often correlated to nutrition supply and stress factors. The annual layers in a tree trunk with millimeter thickness can be directly counted, whereas the layers in tooth cementum with micrometer thickness are made visible using optical microscopy. These optical techniques rely on the surface evaluation or thin, optically transparent slices. Hard X-ray tomography with micrometer resolution, however, provides a three-dimensional view without physical slicing. We have developed a procedure to enhance the tomography data of annual layers in human and bovid tooth cementum. The analysis of a substantial part of an archeological human tooth demonstrated that the detected number of layers depended on the selected region and could vary between 13 and 27. The related average thickness of the annual layers was found to be (5.4 $\pm$ 1.9) $\mu$m for the human tooth, whereas the buffalo tooth exhibited a layer periodicity of 46 $\mu$m. The present study elucidates the potential of combining computational tools with high-quality micro computed tomography data to quantify the annual layers in tooth cementum for a variety of purposes including age-at-death determination., Comment: 16 pages. Event: SPIE Smart Structures + Nondestructive Evaluation, 2022, Long Beach, California, United States

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.

Hard X-ray tomography with Paganin's widespread single-distance phase retrieval filter improves contrast-to-noise ratio (CNR) while reducing spatial resolution (SR). We demonstrate that a Gaussian filter provided larger CNR at high SR with interpretable density measurements for two medically relevant soft tissue samples. Paganin's filter produced larger CNR at low SR, though \emph{a priori} assumptions were generally false and image quality gains diminish for CNR $>1$. Therefore, simple absorption measurements of low-$Z$ specimens combined with Gaussian filtering can provide improved image quality and model-independent density measurements compared to single-distance phase retrieval., Comment: This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Applied Physics Letters 116, 023702 (2020), and may be found at https://aip.scitation.org/doi/10.1063/1.5133742