Micro-Computed Tomography Soft Tissue Biological Specimens Image Data Visualization

Abstract

Visualization of soft tissues in microCT scanning using X-rays is still a complicated matter. There is no simple tool or methodology on how to set up an optimal look-up-table while respecting the type of soft tissue. A partial solution may be the use of a contrast agent. However, this must be accompanied by an appropriate look-up-table setting that respects the relationship between the soft tissue type and the Hounsfield units. The main aim of the study is to determine experimentally derived look-up-tables and relevant values of the Hounsfield units based on the statistical correlation analysis. These values were obtained from the liver and kidneys of 24 mice in solutions of ethanol as the centroid value of the opacity look-up-table area under this graph. Samples and phantom were scanned by a Bruker SkyScan 1275 micro-CT and Phywe XR 4.0 and processed using CTvox and ORS Dragonfly software. To reconstruct the micro-CT projections, NRecon software was used. The main finding of the study is that there is a statistically significant relationship between the centroid of the area under the look-up-table curve and the number of days for which the animal sample was stored in an ethanol solution. H1 of the first hypothesis, i.e. that suggested the Spearman’s correlation coefficient does not equal zero (r1 ≠ 0) regarding this relationship was confirmed. On the other hand, there is no statistically significant relationship between the centroid of the area under the look-up-table curve and the concentration of the ethanol solution. In this case, H1 of the second hypothesis, i.e. that the Spearman’s correlation coefficient does not equal zero (r2 ≠ 0) regarding this relationship was not confirmed. Spearman’s correlation coefficients were −0.27 for the concentration and −0.87 for the number of days stored in ethanol solution in the case of the livers of 13 mice and 0.06 for the concentration and 0.94 for the number of days stored in ethanol solution in the case of kidneys of 11 mice.

Correlative Imaging of Three-Dimensional Cell Culture on Opaque Bioscaffolds for Tissue Engineering Applications

“…3D reconstruction of the GF environment was qualitatively analyzed using CTVol software, and shadow projections were visualized using CTVox software. To highlight the cells versus the GF, cells were false-colored to green with the transfer function editor using the linear interpolation method in CTVox 42 ( Figure S1B ) and by overlaying the falsely colored 3D models in CTVol.…”

Evaluation of Effective Doses of Radiation and Risk Factors in Thorax-Testing CT Scans of Patients with Lung Cancer Cases

“…The HU value for healthy lungs falls between -910 HU and -600 HU [10]. The HU value for soft tissue, meanwhile, lies between 40 and 300 HU [13,14]. Figure 1 shows soft tissue that is out of place or growing abnormally in lung.…”

Deep Learning-Based Segmentation of Post-Mortem Human’s Olfactory Bulb Structures in X-ray Phase-Contrast Tomography

“…Consequently, morphometric data analysis using conventional low-resolution 3D imaging tools [ 6 ] and manual delineation of OB areas are difficult to perform. A number of recent studies have demonstrated that micro-CT is able to provide high-quality images of soft tissue morphology [ 7 ]. However, this imaging technique, which is effective when using staining agents, does not allow soft tissue differentiation based on native tissue contrast.…”