Flowchart of the VIB protocol. The process starts with the import of raw data (upper left). Sections: PREP (light brown): In the steps of preprocessing the imported 3D images are prepared for standardization. These steps include optional resampling and electronic removal of unwanted parts of the 3d images. LAB (light green): During the labeling LabelFields are constructed on the basis of the reference channel; QC1 (light yellow): The first quality control evaluates the LabelFields by basic statistical comparisons of the Material's volumes; RT, LST, CT, DT (light blue): The transformation processes align the Samples to the Template rigidly (RT, LST, CT) or non-rigidly (DT); QC2 (light yellow): The second quality control for the evaluation of the alignment creates MainProbabilityMaps for each file group. These can be controlled visually and statistically; AV (purple): The step of averaging fuses each channel of the 3D images of a file group to an average intensity image. Icons: Ovals: data; squares: processes; diamonds: decisions; hexagon: transformations. Color code: green: 3D images; red: LabelFields; blue: processes/scripts; orange: spreadsheets; yellow: visualization; white: resampled data; hatched: transformed data. Arrows: open: data input to processes; closed: writing data to files.