# Micro-Computed Tomography Soft Tissue Biological Specimens Image Data Visualization
## 2 Materials and Methods
### Materials, Devices, and Software
Some mouse organs, such as liver, kidney, brain, heart, and leg, were kept for one week in a solution of potassium iodide with concentration 100 mM (KI, Merck, Czech Republic) in 20% ethanol before scanning. Lastly, the database included corrosive preparations in which a resin (Mercox) [10] was infused into the vascular system and allowed to harden, the remaining tissue was then dissolved in lye by maceration and the sample was scanned. Corrosive preparations of rabbit and rat lung and heart were selected for the purpose of this study. For the implementation of the idea of blood vessels visualization in soft tissue using the contrast that would be created by the presence of air in the vascular cavities, chicken flesh was used as a phantom in which cylindrical tubes/capillaries of various diameters made of different materials were placed. These were two tubes (silicone), a glass capillary with sealed ends, and a plastic straw (bioplastic PLA). This phantom, depicted in Figure 1, was then scanned with the Phywe XR 4.0 (PHYWE Systeme GmbH & Co. KG, Gottingen, Germany) experimental setup. Two \(\upmu\)CT systems were used to scan the above samples. The ex vivo chicken samples were scanned with a professional \(\upmu\)CT system Bruker SkyScan 1275 located at the Department of Anatomy, 3 rd Faculty of Medicine, Charles University, while the Phywe XR 4.0 experimental setup was used to scan the phantom of the chicken vasculature and capillaries at the Dept. of Biomedical Technology, Fac. of Biomedical Engineering, Czech Technical University in Prague. Bruker's SkyScan 1275 has been specifically designed for fast scanning using advances in X-ray source technology and efficient flat-panel detectors. This X-ray source has the selectable anode voltage of the assembly ranging from 20 to 100 kV and the max. available power is 10 W. The assembly includes an active 3 megapixel CMOS flat-panel detector with a maximum possible resolution of up to 4 \(\upmu\)m (at maximum magnification) and it is capable of accommodating a sample diameter of 96 mm and a height of 120 mm. All used setups of the above mentioned \(\upmu\)CT are available within the Appendix B, i.e., Tables A2-A19. The XR 4.0 experimental setup from the German company Phywe was designed for teaching purposes and for laboratory experiments with X-rays. Its advantage lies, among other things, in the relatively easy and quick interchangeability of the X-ray tube and, therefore, facilitates experiments with different anode materials [11; 12]. The XR 4.0 can also be used as a \(\upmu\)CT system thanks to an expansion kit supporting the computed tomography function. This set consists of a fixed copper X-ray tube that illuminates the specimen on a rotary table driven by a stepper motor with a minimum adjustable table rotation angle of 0.086\({}^{\circ}\). The attenuated X-ray radiation is then incident on an XRIS detector (CMOS) with an active area of 5 \(\times\) 5 cm\({}^{2}\) and a maximum possible resolution of 48 \(\upmu\)m [11; 12]. The selectable anode voltage of the assembly is 5-35 kV with an adjustable emission current in the range up to 1 mA. Setup with detailed setting is available within the Appendix B, i.e., Table A1. As regards the software, CTvox (Version 3.3.1, 3D.SUITE Software, Bruker MicroCT, Kontich, Belgium) [13] and ORS Dragonfly (Version 2020.2 Build 941, Montreal, QC, Canada) [14] software were used for suitable visualization. Within an additional part of the study there were used NRecon (Version 1.7.4.2, Bruker MicroCT, Kontich, Belgium) [15] and Measure CT (Version 2.0, PHYWE Systeme GmbH & Co. KG, Gottingen, Germany) [12]  
Figure 1: Chicken sample with capillaries as vascular phantom (**top**) and phantom X-ray image (**bottom**); materials from left: bioplastic PLA, glass, green silicone, and transparent silicone. Scale is in [cm]. software to reconstruct the \(\mu\)CT projections. Software MIPS (Version 2.0, Czech Technical University in Prague, Faculty of Biomedical Engineering, Kladno, Czech Republic) [16] was used for illustration purposes only.