Sample preparation

Often overlooked, but of great importance is the sample preparation. Not only the positioning of the sample in the microCT scanner, which will allow you to obtain the desired pixel size, but also the stability of the sample throughout the scan is crucial. Samples such as fibers or micro-spheres can be stably mounted on the provided metal sample holders by using a small drop of glue. After the glue is dry, this easy and straightforward technique will enable long scans without sample movement. If the samples are preserved in ethanol of formaldehyde, placing them directly on a stage will allow the liquid to evaporate during the scan, resulting in artefacts in the reconstructed images. Leaving the sample surrounded by liquid will increase the noise in the image and will impact the beam hardening. By wrapping the samples in parafilm or low dense wax, thereby creating a ‘cocoon’, will prevent this.

However, for a wide range of samples the density difference between internal structures is sometimes not enough. For these samples a chemical drying procedure can be useful. In the method note "MN070 chemical drying of specimens to enhance contrast" you can find more information on how this simple technique works. This drying process has been successfully used in a range of biological samples. A nice example of this technique is lungs scanned ex vivo, where without this drying the fixative would limit the contrast. After chemical drying the contrast between the tissue and the air is maximized, resulting in much nicer images. Although maybe not considered straightforward, this procedure can also be applied to soft tissues. The image below shows the result of the chemical drying of a snake, where there is a differential uptake of the chemical allowing visualization of the different soft tissues.

Sagittal (upper) and coronal (lower) virtual slices through the head of a snake scanned at 8μm pixel size