Comparison of Standard Brains created with four different standardization algorithms. Average intensity maps of the pattern channel (line 1+2) display the typical expression pattern of the Gal4 driver line, while average intensity maps of the reference channel (line 3) display the typical morphology of the file group, visualized using the antibody nc82. Brightness is coded in false colors. The difference in fuzziness and the volume of uniformly bright areas can be taken as a measure for alignment quality. MainProbabilityMaps reflect the distribution of the Materials of a file group after transformation (in %). False color coded areas with maximum probability of occurrence of a Material (Material overlaps in all Samples, core) are red, areas outside Materials are blue (see false color scheme). Using the same set of data, one can take the ratio between the core and the area of low probability of occurrence of a Material (seam) as a measure of transformation quality. No MainProbabilityMap is generated for the AmiraRegistrationTransformation because this method does not use LabelFields for the alignment of the Samples but the distribution of the grey values in the 3D images. 1st line: (1a-d): Medial frontal section through a standardized Gal4 expression pattern. The section lies posterior to the horizontal lobes, crosses the tip of the α/α'-lobes (α) the peduncle (p) and the ellipsoid body (e), which is not stained in 201y. 2nd line (2a-d): Direct volume rendering of standardized Gal4 expression patterns. 3rd line (3a-d): Direct Volume Rendering of standardized nc82-reference patterns. 4th line (4b-d): MainProbabilityMap at the same level as 1b-d. The uppermost dots represent the tip of the α/α'-lobes, the dots beneath are cross sections of the mushroom body peduncles. In the optic lobes the section runs through the medulla, the lobula and the very tip of the right lobula plate. Figs. 1-3: Averaged intensities color coded. Figs. 4b-d: Material's probabilities of occurrence color coded. n = 12. Flies: female Gal4-201y × UAS:mcd8GFP.