Single subject coronal images of the E16, P0, and adult mouse brains from the mouse brain database. At each stage, the brain specimen with the median total brain volume was shown. The images are overlaid with reconstructed white and gray matter structures currently included in the atlas. The color schemes for gray matter structures in the T₂ and FA images are: white: neocortex (cortical plates in the E16 mouse brain); blue: hippocampus (hippocampal neuroepithelium in the E16 mouse brain); purple: striatum. The color schemes for White matter structures are: yellow: fimbria (fi); pink: corpus callosum (cc); magenta: fasciculus retroflexus (fr); red: stria terminalis (st); light green: fornix (fx); dark green: the trigeminal nerve (5n); light blue: cerebral peduncle (cp); dark blue: stria medularis (sm); light purple: mammillothalamic tract (mt); purple: optic tract (opt).

Development of the white matter tracts related to the cerebellum and thalamus. At each stage,single subject images from the brain specimen with the median total brain volume was shown. A) The middle cerebellar peduncle (mcp, green), the internal capsule and cerebral peduncle (cp, red), together with the caudate putamen (CPu), neuroepithelium of the caudate putamen (CPuNE, only at E16), hippocampus (H), and cerebellum (CB). Time-related changes in the cross-sectional areas of the cerebral peduncle and middle cerebellar peduncle are examined at selected coronal sections (inside the red and green boxes, respectively). The locations of the coronal sections along the Y axis (the anterior-posterior axis) are marked in each image, and also indicated by the red and green arrows in the 3D images. B) White matter tracts that pass through the thalamus, including the fasciculus retroflexus (fr), the stria medularis (sm, blue), the fornix (f, light blue), the stria terminalis (st, orange), and the mammalothalamic tract (mt, red), together with the caudate putamen (CPu), and the hippocampus (H). Time-related changes in the cross-sectional areas of the stria medularis (sm) and the fasciculus retroflexus (fr) are examined at selected horizontal sections, as indicated by the green and blue arrows in the 3D images. In the 2D images, boundaries of the white matter tracts in the adult brains are defined and overlaid on the images from P0 and P7 mouse brains. Scale bars = 1 mm.

Changes in white matter cross-sectional areas in twelve major white matter tracts. The area data were fitted to a sigmoidal model and the 95% confidence intervals are shown in the figures, with figure background indicative of the percentile of the estimated adult values (parameter a in Table 3). Structural abbreviations are: ac: anterior commissure; hc: hippocampal commissure; cc: corpus callosum; cp: cerebral peduncle; 5n: the trigeminal nerve; 7n: the facial nerve; st: stria terminalis; sm: stria medularis; fr: fasciculus retroflexus; fx: fornix; mcp: middle cerebellar peduncle; icp: inferior cerebellar peduncle.

Development of the cranial nerves and commissural tracts in the mouse brain. At each stage,single subject images from the brain specimen with the median total brain volume was shown. A) The trigeminal nerve (5n, green), facial nerve (7n, yellow), vestibulocochlear nerve (8n, light blue), optic nerve (red), and optic tracts (purple), together with the lateral ventricles (LV, blue) and cerebellum (CB, green). To facilitate comparison between different specimens, we define the mid-sagittal anterior commissure as the origin, with the X, Y, and Z axes along the left-right, anterior-posterior, superior-inferior axes as shown by the white arrows in the 3D rendering of the adult mouse brain. Time-related changes in cross-sectional areas of the 5^th nerves and optic nerves are examined in coronal sections (inside the green and red boxes, respectively). The locations of the coronal sections along the Y axis (anterior-posterior) are marked under each image, and also indicated by the green and red arrows in the 3D images. B) The anterior commissure (ac, green), hippocampal commissure and fimbria (hc/fi, red), with the lateral ventricles (blue), hippocampus (H, light blue), and cerebellum (CB, green) in P0 and adult mouse brains. The white arrows indicate the corpus callosum. Time-related changes in cross-sectional areas of the commissural fibers are examined at the mid-sagittal level. No embryonic data are shown in panel B because commissural and cerebellar tracts were not visible in MR images until late embryonic stages. The locations of the sagittal sections along the X axis (the left-right axis, x=0 for the mid-sagittal section) are indicated by the dark green arrows in the 3D images Scale bars = 1 mm.

Volumes of the whole brain, neocortex, hippocampus, and cerebellum (left vertical axis) and their percentage of adult volumes (right vertical axis). The volume measurements were fitted to a sigmoidal model with 95% confidence band (long dash lines) and 95% prediction band (short dash lines). The right vertical axis shows the percentile of the estimated adult values (parameter a in Table 2).

Top: Population average T₂, directional encoded colormap (DEC) images of the P7, P21, and P60 mouse brain and maps of segmentation and maps of anatomical variation overlaid with outlines of structural segmenations. The unit in the variation maps is mm². Bottom: anatomical variations in the P60 mouse brain rendered on the surfaces of the neocortex, hippocampus, lateral ventricles, and striatum.