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. 2023 Jun 12;9(7):1026–1033. doi: 10.1038/s41477-023-01439-4

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© The Author(s) 2023

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. 2 — a, PHYTOMap data analysis pipeline for single-cell analysis. b, 3D visualization of transcripts detected and decoded after image registration in a representative root tip (root 4). A middle section (z planes 90–120 of 208) of the image is displayed. Representative genes from each imaging round are shown. c, Violin plots showing the number of unique RNA molecules (left) and genes (right) detected in five root tip samples. d, Left, scatter plot comparing normalized bulk expression of each gene between two samples (root 1 and root 2). Right, correlation plot showing pair-wise correlation coefficients among five replicates. e, Hierarchical clustering of cells of root 4 based on the relative expression of 28 genes. Cluster IDs are indicated at the bottom. RE, relative expression. f, UMAP visualization of the clusters shown in e. g, 3D visualization of transcripts coloured by clusters in e and f in a representative root tip (root 4). A middle section (z planes 90–120 of 208) of the image is displayed. Scale bar, 25 μm (b,g).