Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering

Table 4 Comparison of clustering results with the Reference Atlas annotations at developmental ontology Level 3

Measures	Clustering	E11.5	E13.5	E15.5	E18.5	P4	P14	P28	Average
	k-means	0.4173	0.3754	0.3882	0.3620	0.3633	0.3480	0.3455	0.3714
NMI	PCA₂	0.2545	0.1508	0.1777	0.2344	0.2101	0.2631	0.2718	0.2232
NMI	PCA₁₀	0.3831	0.3305	0.3310	0.3045	0.3315	0.3094	0.3247	0.3307
	t-SNE₂	0.5337	0.4947	0.5097	0.3977	0.3556	0.3481	0.3637	0.4290
	t-SNE₁₀	0.5469	0.5202	0.5065	0.4382	0.4420	0.3484	0.3947	0.4567
	k-means	0.5820	0.5751	0.5605	0.5815	0.5889	0.6838	0.5839	0.5937
S-index	PCA₂	0.6524	0.6869	0.6206	0.6413	0.6399	0.6790	0.6283	0.6498
S-index	PCA₁₀	0.6065	0.6547	0.6270	0.6050	0.6278	0.6982	0.6113	0.6329
	t-SNE₂	0.4729	0.5132	0.5387	0.5256	0.5889	0.6736	0.6383	0.5645
	t-SNE₁₀	0.4724	0.4941	0.5736	0.5968	0.5566	0.6653	0.5673	0.5609
	k-means	0.1756	0.1516	0.1341	0.1242	0.0609	0.0571	0.0634	0.1096
ARI	PCA₂	0.0849	0.0235	0.0066	0.0327	0.0190	0.0386	0.0499	0.0364
ARI	PCA₁₀	0.1839	0.1175	0.0980	0.0700	0.0581	0.0388	0.0531	0.0885
	t-SNE₂	0.2654	0.1967	0.1670	0.1021	0.0823	0.0779	0.0788	0.1386
	t-SNE₁₀	0.2699	0.2123	0.1521	0.1195	0.0902	0.0847	0.0965	0.1464
	k-means	0.3854	0.5233	0.6028	0.6135	0.6853	0.7253	0.7090	0.6064
Purity	PCA₂	0.3127	0.3825	0.4584	0.5190	0.6056	0.6594	0.6473	0.5121
Purity	PCA₁₀	0.3918	0.4835	0.5596	0.5560	0.6708	0.6856	0.6892	0.5766
	t-SNE₂	0.4774	0.5824	0.6772	0.6082	0.6795	0.7072	0.7121	0.6349
	t-SNE₁₀	0.4895	0.6081	0.6473	0.6392	0.7305	0.7306	0.7342	0.6542

ISSN: 1471-2105