Fig. 3: Example of landmarks used for atlas parcellation at E13.5.

The E13.5 DevCCF includes 6 aligned 3D whole brain images: an LSFM Autofluorescence template, 4 MRI contrast templates, and developmental annotations. We show each template as horizontal (a–f), coronal (g–l), and sagittal (m–r) cross sections with a selected set of visible landmarks that guided atlas segmentation. Selected landmarks are noted, including the dark ventricles marked in the LSFM template (a, g, m), telencephalic intermediate and superficial layers with inverse contrasts in DWI and FA templates (c, d), the telencephalic periventricular zone in the T2w template (e, k, q), the retroflex tract that denotes the boundary between prosomeres (p)2 and 3 in DWI and FA templates (j, o, p), and distinct diencephalic prosomeres 1, 2, and 3 in MRI ADC and DWI templates (h, i), the cerebellum in all sagittal viewed templates (m–r). Scale bar = 3 mm. 6M abducens motor nucleus, 3M occulomotor nucleus. Annotation colors are defined in DevCCF ontology (Supplementary Data 2).