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Abstract BackgroundGiven the need for descriptive and increasingly mechanistic morphological analyses, contrast‐enhanced microcomputed tomography (microCT) represents perhaps the best method for visualizing 3D biological soft tissues in situ. Although staining protocols using phosphotungstic acid (PTA) have been published with beautiful visualizations of soft tissue structures, these protocols are often aimed at highly specific research questions and are applicable to a limited set of model organisms, specimen ages, or tissue types. We provide detailed protocols for micro‐level visualization of soft tissue structures in mice at several embryonic and early postnatal ages using PTA‐enhanced microCT. ResultsOur protocols produce microCT scans that enable visualization and quantitative analyses of whole organisms, individual tissues, and organ systems while preserving 3D morphology and relationships with surrounding structures, with minimal soft tissue shrinkage. Of particular note, both internal and external features of the murine heart, lungs, and liver, as well as embryonic cartilage, are captured at high resolution. ConclusionThese protocols have broad applicability to mouse models for a variety of diseases and conditions. Minor experimentation in the staining duration can expand this protocol to additional age groups, permitting ontogenetic studies of internal organs and soft tissue structures within their 3D in situ position. 

Abstract ObjectivesVariation in human trabecular bone morphology can be linked to habitual behavior, but it is difficult to investigate in vivo due to the radiation required at high resolution. Consequently, functional interpretations of trabecular morphology remain inferential. Here we introduce a method to link low‐ and high‐resolution CT data from dry and fresh bone, enabling bone functional adaptation to be studied in vivo and results compared to the fossil and archaeological record. Materials and methodsWe examine 51 human dry bone distal tibiae from Nile Valley and UK and two pig tibiae containing soft tissues. We compare low‐resolution peripheral quantitative computed tomography (pQCT) parameters and high‐resolution micro CT (μCT) in homologous single slices at 4% bone length and compare results to our novel Bone Ratio Predictor (BRP) method. ResultsRegression slopes between linear attenuation coefficients of low‐resolution pQCT images and bone area/total area (BA/TA) of high‐resolution μCT scans differ substantially between geographical subsamples, presumably due to diagenesis. BRP accurately predicts BA/TA (R²= .97) and eliminates the geographic clustering. BRP accurately estimates BA/TA in pigs containing soft tissues (R²= 0.98) without requiring knowledge of true density or phantom calibration of the scans. DiscussionBRP allows automated comparison of image data from different image modalities (pQCT, μCT) using different energy settings, in archeological bone and wet specimens. The method enables low‐resolution data generated in vivo to be compared with the fossil and archaeological record. Such experimental approaches would substantially improve behavioral inferences based on trabecular bone microstructure.