arXiv subjects

Griffin Rodgers

Publications and source records attributed to Griffin Rodgers.

5 recordsLinked to original sources

arXiv2025

In vivo imaging of central nervous system fluid spaces using synchrotron radiation-based micro computed tomography

Current approaches to in vivo imaging of the mouse central nervous system (CNS) do not offer a combination of micrometer resolution and a whole-brain field of view. To address this limitation, we introduce an approach based on synchrotron radiation-based hard X-ray micro computed tomography (SR$\mu$CT). We performed intravital SR$\mu$CT acquisitions of mouse CNS fluid spaces at three synchrotron radiation facilities. Imaging was conducted on both anesthetized free-breathing and ventilated animals, with and without retrospective cardiac gating. We achieved whole-brain imaging at 6.3 $\mu$m uniform voxel size, observed the distribution of cerebrospinal fluid (CSF) contrast agent over time and quantified choroid plexus movement. SR$\mu$CT bridges the gap between multiphoton microscopy and magnetic resonance imaging, offering dynamic imaging with micrometer-scale resolution and whole-organ field of view. Intravital SR$\mu$CT will play a crucial role in validating and integrating hypotheses on CSF dynamics and solute transport by providing unique data that cannot be acquired otherwise.

physics.med-ph↗

arXiv2024

Synchrotron radiation-based tomography of an entire mouse brain with sub-micron voxels: augmenting interactive brain atlases with terabyte data

Synchrotron radiation-based X-ray microtomography is uniquely suited for post mortem three-dimensional visualization of organs such as the mouse brain. Tomographic imaging of the entire mouse brain with isotropic cellular resolution requires an extended field-of-view and 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. We present extended-field X-ray microtomography with 0.65 $\mu$m voxel size covering an entire mouse brain. The 4,495 projections from 8 x 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. The data were transformed block-wise and 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. 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 3.3-teravoxel dataset is publicly available and easily accessible for domain experts via browser-based viewers.

physics.med-ph↗

arXiv2022

Three-dimensional imaging of porcine joint tissues down to the subcellular level

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.

physics.med-ph↗

arXiv2022

Three-dimensional imaging and analysis of annual layers in tree trunk and tooth cementum

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.

physics.bio-ph↗

arXiv2019

Optimizing contrast and spatial resolution in hard X-ray tomography of medically relevant tissues

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.

physics.med-ph↗