Quantifying the tissue shrinkage caused by sample preparation for micro-CT and LSFM

Aims Micro Computed Tomography (micro-CT) and light sheet fluorescence microscopy (LSFM) are often used tomographic methods for imaging macroscopic samples with histological detail. It is even possible to image multiple tissue types simultaneously (e.g. bone, muscle, nerve and fat tissue). However, micro-CT requires staining with heavy elements (and thus fixation and sometimes dehydration) to distinguish soft tissue. LSFM also involves fixation, dehydration and staining, and additionally requires decalcification and clearing. In both preparation methods, the sample is prone to shrinkage, which is often not mentioned, let alone quantified. Therefore, our aim is to quantify and compare tissue shrinkage of 3 micro-CT stains (PTA, IKI and I2E) and the LSFM preparation in bone, muscle and brain tissue.