Stahl, P. L. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78–82 (2016).

Article  CAS  PubMed  Google Scholar 

Bergenstrahle, J., Larsson, L. & Lundeberg, J. Seamless integration of image and molecular analysis for spatial transcriptomics workflows. BMC Genomics 21, 482 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Stickels, R. R. et al. Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nat. Biotechnol. 39, 313–319 (2021).

Article  CAS  PubMed  Google Scholar 

Rodriques, S. G. et al. Slide-seq: a scalable technology for measuring genome-wide expression at high spatial resolution. Science 363, 1463–1467 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu, Y. et al. High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell 183, 1665–1681.e18 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sergio Marco, S. et al. Optimizing xenium in situ data utility by quality assessment and best practice analysis workflows. Preprint at https://www.biorxiv.org/content/10.1101/2023.02.13.528102v1 (2023).

He, S. et al. High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging. Nat. Biotechnol. 40, 1794–1806 (2022).

Article  CAS  PubMed  Google Scholar 

Zhang, M. et al. Molecularly defined and spatially resolved cell atlas of the whole mouse brain. Nature 624, 343–354 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Slovin, S. et al. Single-cell RNA sequencing analysis: a step-by-step overview. Methods Mol. Biol. 2284, 343–365 (2021).

Article  CAS  PubMed  Google Scholar 

Cho, C.-S. et al. Microscopic examination of spatial transcriptome using Seq-Scope. Cell 184, 3559–3572.e22 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

10x Genomics. Visium HD: whole transcriptome spatial discovery at the resolution you need. https://www.10xgenomics.com/library/8012d2 (accessed 25 February 2024).

Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell 185, 1777–1792.e21 (2022).

Article  CAS  PubMed  Google Scholar 

Fu, X. et al. Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain. Cell 185, 4621–4633.e17 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Macosko, E. Z. et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 161, 1202–1214 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

BD_Biosciences BD Rhapsody™ system—mRNA whole transcriptome analysis (WTA) library preparation protocol. https://scomix.bd.com/hc/article_attachments/13726971063565 (2022).

Salmen, F. et al. Barcoded solid-phase RNA capture for spatial transcriptomics profiling in mammalian tissue sections. Nat. Protoc. 13, 2501–2534 (2018).

Article  CAS  PubMed  Google Scholar 

10x Genomics. Visium spatial tissue optimization reagents kits user guide. https://www.10xgenomics.com/support/spatial-gene-expression-fresh-frozen/documentation/steps/tissue-optimization/visium-spatial-tissue-optimization-reagents-kits-user-guide (2022).

10x Genomics. Visium spatial gene expression reagent kits user guide. https://www.10xgenomics.com/support/spatial-gene-expression-fresh-frozen/documentation/steps/library-construction/visium-spatial-gene-expression-reagent-kits-user-guide (2023).

Kaminow, B., Yunosov, D. & Dobin, A. STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data. Preprint at https://www.biorxiv.org/content/10.1101/2021.05.05.442755v1 (2021).

Xi, J., Lee, J. H., Kang, H. M. & Jun, G. STtools: a comprehensive software pipeline for ultra-high-resolution spatial transcriptomics data. Bioinform. Adv. 2, vbac061 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Do, T. H. et al. TREM2 macrophages induced by human lipids drive inflammation in acne lesions. Sci. Immunol. 7, eabo2787 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ma, F. et al. Single cell and spatial sequencing define processes by which keratinocytes and fibroblasts amplify inflammatory responses in psoriasis. Nat. Commun. 14, 3455 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hsu, J. et al. High-resolution spatial transcriptomic atlas of mouse soleus muscle: unveiling single cell and subcellular heterogeneity in health and denervation. Preprint at https://www.biorxiv.org/content/10.1101/2024.02.26.582103v1 (2024).

Poovathingal, S. et al. Nova-ST: Nano-patterned ultra-dense platform for spatial transcriptomics. Cell Rep. Methods 4, 100831 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schott, M. et al. Open-ST: high-resolution spatial transcriptomics in 3D. Cell 187, 3953–3972.e26 (2024).

Article  CAS  PubMed  Google Scholar 

Bahar Halpern, K. et al. Nuclear retention of mRNA in mammalian tissues. Cell Rep. 13, 2653–2662 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gurkar, A. U. et al. Spatial mapping of cellular senescence: emerging challenges and opportunities. Nat. Aging 3, 776–790 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cao, J. et al. Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-02086-y (2024).

Bai, Z. et al. Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues. Cell https://doi.org/10.1016/j.cell.2024.09.001 (2024).

Wulf, M. G. et al. Non-templated addition and template switching by Moloney murine leukemia virus (MMLV)-based reverse transcriptases co-occur and compete with each other. J. Biol. Chem. 294, 18220–18231 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hughes, T. K. et al. Second-strand synthesis-based massively parallel scRNA-seq reveals cellular states and molecular features of human inflammatory skin pathologies. Immunity 53, 878–894.e7 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hao, Y. et al. Dictionary learning for integrative, multimodal and scalable single-cell analysis. Nat. Biotechnol. 42, 293–304 (2024).

Article  CAS  PubMed  Google Scholar 

Si, Y. et al. FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics. Nat. Methods 21, 1843–1854 (2024).

Article  CAS  PubMed  Google Scholar 

Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Pierre, S. & Luc, M. V. Determining watersheds in digital pictures via flooding simulations. Proc. SPIE Int. Soc. Opt. Eng. 1360, 240–250 (1990).

Google Scholar 

Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods 18, 100–106 (2021).

Article  CAS  PubMed  Google Scholar 

Pachitariu, M. & Stringer, C. Cellpose 2.0: how to train your own model. Nat. Methods 19, 1634–1641 (2022).

Article  CAS