Fig. 5: Profiling mouse 3D brain atlas. | Nature Communications

Fig. 5: Profiling mouse 3D brain atlas.

From: DECIPHER for learning disentangled cellular embeddings in large-scale heterogeneous spatial omics data

Fig. 5

a Diagram illustrating the mouse brain atlas in 3D CCF coordinates54. b UMAP visualization of DECIPHER molecular identity embeddings on the mouse brain atlas. c UMAP visualization of DECIPHER spatial context embeddings on the mouse brain atlas when using 3D coordinates (left panel) or only 2D coordinates (right panel). d Distribution density of every cell type on UMAP result based on DECIPHER spatial context embedding. Astro astrocyte, AQ aqueduct of Sylvius, CB cerebellum, CGE caudal ganglionic eminence, CNU cerebral nuclei, CR Cajal–Retzius, CT corticothalamic, CTX cerebral cortex, CTXsp cortical subplate, DG dentate gyrus, EA extended amygdala, Epen ependymal, EPI epithalamus, ET extratelencephalic, GC granule cell, HB hindbrain, HPF hippocampal formation, HY hypothalamus, HYa anterior hypothalamic, IMN immature neurons, IT intratelencephalic, L6b layer 6b, LGE lateral ganglionic eminence, LH lateral habenula, LSX lateral septal complex, MB midbrain, MGE medial ganglionic eminence, MH medial habenula, MM medial mammillary nucleus, MY medulla, NP near-projecting, OB olfactory bulb, OEC olfactory ensheathing cells, OLF olfactory areas, Oligo oligodendrocytes, OPC oligodendrocyte precursor cells, P pons, PAL pallidum, STR striatum, TH thalamus, V3 third ventricle, V4 fourth ventricle, VL ventral lateral nucleus, CM centromedian nucleus, EPS entorhinal-perirhinal-solitary complex, IFBS internal fiber bundles, MFBS medial forebrain bundles, SCWM sub-cortical white matter. Neurotransmitter types: DOPA dopaminergic, GABA GABAergic, Glut glutamatergic, Nora noradrenergic, Sero serotonergic36.

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