FICTURE: scalable segmentation-free analysis of submicron-resolution spatial transcriptomics

Bressan, D., Battistoni, G. & Hannon, G. J. The dawn of spatial omics. Science 381, eabq4964 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Moses, L. & Pachter, L. Museum of spatial transcriptomics. Nat. Methods https://doi.org/10.1038/s41592-022-01409-2 (2022).Kang, H. M. & Lee, J. H. Spatial single-cell technologies for exploring gastrointestinal tissue transcriptome. Compr. Physiol. https://doi.org/10.1002/cphy.c210053 (2023).Ståhl, P. L. et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science 353, 78–82 (2016).Article 
PubMed 

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 
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 
Vickovic, S. et al. High-definition spatial transcriptomics for in situ tissue profiling. Nat. Methods 16, 987–990 (2019).Article 
CAS 
PubMed 
PubMed Central 

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 
Chen, A. et al. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell https://doi.org/10.1016/j.cell.2022.04.003 (2022).Article 
PubMed 
PubMed Central 

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 
Zhang, M. et al. Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH. Nature 598, 137–143 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Janesick, A. et al. Hiigh resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis. Nat. Commun. 14, 8353 (2022).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 
Beucher, S. The watershed transformation applied to image segmentation. Scanning Microsc. 6, 299–314 (1992).
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 
Palla, G. et al. Squidpy: a scalable framework for spatial omics analysis. Nat. Methods 19, 171–178 (2022).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Dries, R. et al. Giotto: a toolbox for integrative analysis and visualization of spatial expression data. Genome Biol. 22, 78 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e29 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Long, Y. et al. Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST. Nat. Commun. 14, 1155 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Gruner, H. N. & McManus, M. T. Examining the evidence for extracellular RNA function in mammals. Nat. Rev. Genet. 22, 448–458 (2021).Article 
CAS 
PubMed 

Google Scholar 
Sacher, F., Feregrino, C., Tschopp, P. & Ewald, C. Y. Extracellular matrix gene expression signatures as cell type and cell state identifiers. Matrix Biol. Plus 10, 100069 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Park, J. et al. Cell segmentation-free inference of cell types from in situ transcriptomics data. Nat. Commun. 12, 3545 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
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 
Petukhov, V. et al. Cell segmentation in imaging-based spatial transcriptomics. Nat. Biotechnol. 40, 345–354 (2022).Article 
CAS 
PubMed 

Google Scholar 
Littman, R. et al. Joint cell segmentation and cell type annotation for spatial transcriptomics. Mol. Syst. Biol. 17, e10108 (2021).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Miller, B. F., Huang, F., Atta, L., Sahoo, A. & Fan, J. Reference-free cell type deconvolution of multi-cellular pixel-resolution spatially resolved transcriptomics data. Nat. Commun. 13, 2339 (2022).Article 
CAS 
PubMed 
PubMed Central 

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 
Birkl, D. et al. TNF-α promotes mucosal wound repair through enhanced platelet activating factor receptor signaling in the epithelium. Mucosal Immunol. 12, 909–918 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Leoni, G., Neumann, P.-A., Sumagin, R., Denning, T. L. & Nusrat, A. Wound repair: role of immune-epithelial interactions. Mucosal Immunol. 8, 959–968 (2015).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Schaum, N. et al. Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature 562, 367–372 (2018).Article 
PubMed Central 

Google Scholar 
Blondel, V. D., Guillaume, J.-L., Lambiotte, R. & Lefebvre, E. Fast unfolding of communities in large networks. J. Stat. Mech. Theory Exp. 2008, P10008 (2008).Article 

Google Scholar 
Traag, V. A., Waltman, L. & van Eck, N. J. From Louvain to Leiden: guaranteeing well-connected communities. Sci. Rep. 9, 5233 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Bora, P. & Majumdar, A. S. Adipose tissue-derived stromal vascular fraction in regenerative medicine: a brief review on biology and translation. Stem Cell Res. Ther. 8, 145 (2017).Article 
PubMed 
PubMed Central 

Google Scholar 
Choi, J., Cha, Y. J. & Koo, J. S. Adipocyte biology in breast cancer: from silent bystander to active facilitator. Prog. Lipid Res. 69, 11–20 (2018).Article 
CAS 
PubMed 

Google Scholar 
Anderson, N. M. & Simon, M. C. The tumor microenvironment. Curr. Biol. 30, R921–R925 (2020).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Liu, C. C. et al. Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering. Nat. Commun. 14, 4618 (2023).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Blei, D. M., Kucukelbir, A. & McAuliffe, J. D. Variational inference: a review for statisticians. J. Am. Stat. Assoc. 112, 859–877 (2017).Article 
CAS 

Google Scholar 
Chen, D. et al. Measuring and relieving the over-smoothing problem for graph neural networks from the topological view. AAAI 34, 3438–3445 (2020).Article 

Google Scholar 
Hoffman, M. D., Blei, D. M., Wang, C. & Paisley, J. Stochastic variational inference. J. Mach. Learn. Res. 14, 1303–1347 (2013).Blei, D. M., Ng, A. Y. & Jordan, M. I. Latent Dirichlet allocation. J. Mach. Learn. Res. 3, 993–1022 (2003).
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 
Xu, Z. et al. STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization. Nucleic Acids Res. 52, 1053–1061 (2023).Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).Article 
CAS 
PubMed 
PubMed Central 

Google Scholar 
Si, Y. Data from “FICTURE: scalable segmentation-free analysis of sub-micron resolution spatial transcriptomics” (1.0). Zenodo https://doi.org/10.5281/zenodo.10070621 (2023).