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. 2023 Dec 13;624(7991):317–332. doi: 10.1038/s41586-023-06812-z

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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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 2 — (a) Workflow for generating and processing MERFISH data. (b) Correlation of gene detection between MERFISH and bulk RNA-sequencing for four different brain regions. (c) Histogram displaying the distribution of gene detection correlation between adjacent MERFISH sections. (d-f) Violin plots displaying distribution of cell volumes (d), gene detection (e), and mRNA molecule detection (f) for individual sections ordered from anterior to posterior (left panel) or cumulative distribution for the whole brain (right panel). Red dashed lines indicate cutoff for filtering. (g) Cumulative histogram showing the relative contribution of each subclass to each section ordered from anterior to posterior. (h) Heatmap showing the proportion of cells per region for each subclass in the MERFISH data (left) and scRNA-seq data (right). The heatmap in the middle shows the correlation between region distribution of MERFISH and scRNA-seq data.