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. 2022 Oct 17;13:6118. doi: 10.1038/s41467-022-33758-z

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a Datasets acquired using different technologies (Smart-seq2, 10X, and Microwell-seq) covering various tissues used for construction of the mouse atlas. b UMAP embeddings of the Mouse Atlas dataset colored by batch and tissue. c UMAP embeddings of the Mouse Atlas after SCALEX integration, colored by cell-type. d Scatter plot showing a quantitative comparison of the ARI score (y-axis) and the NMI score (x-axis) based-on the Leiden clustering results on the latent space based on the Human Atlas, Mouse Atlas, and Human Fetal Atlas datasets. e Comparison of over-correction score by the indicated methods based on the Human Atlas, Mouse Atlas, and Human Fetal Atlas datasets. f UMAP embeddings of the common cell space obtained by using SCALEX to project the two Tabula Muris Senis data batches and two mouse tissues (lung and kidney) data batches onto the Mouse Atlas dataset. Cells are colored by cell-type with light gray shadows representing the original Mouse Atlas dataset. g Confusion matrix of the cell-type annotations by SCALEX and those in the original studies. Color bar represents the percentage of cells in confusion matrix C_ij known to be cell-type i and predicted to be cell-type j.