STAMP workflow and downstream analysis (IMAGE)
Caption
Figure 1. STAMP workflow and downstream analysis. Dissociated cells or nuclei are immobilized on a slide, imaged (RNA +/- protein), and exported as an analysis-ready cell × feature matrix linked to per-cell morphology and coordinates. Downstream Python analysis applies standard single-cell steps (QC, normalization, embedding/latent modeling, clustering/label transfer, morpho-transcriptomic analysis, and interpretation), with results traceable back to the images. STAMP: single-cell transcriptomics analysis and multimodal profiling; QC: quality control; PBMC: peripheral blood mononuclear cell; PCA: principal component analysis; UMAP: Uniform Manifold Approximation and Projection; DE: differential expression; scVI: single-cell variational inference; scANVI: single-cell ANnotation using variational inference.
Credit
© Suresh Poudel*,Felipe Segato Dezem,Luciano G. Martelotto ,Jasmine T. Plummer,Douglas R. Green* 2026. This is an Open Access article licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, sharing, adaptation, distribution and reproduction in any medium or format, for any purpose, even commercially, 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.
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CC BY