ArticleNature methods2025
Cell simulation as cell segmentation.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
48 citing papers in PubMed.
- Reprogramming engineered autologous T cells to overcome resistance in patients with Merkel cell carcinoma.Science translational medicine · 2026Trial
- Spatial Transcriptomics Analysis of Ewing Sarcoma.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Human adult and pediatric multimodal transcriptomic atlas of progression from pressure-loaded to failing right ventricle.Nature cardiovascular research · 2026Article
- Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial-immune cell interactions.Nature immunology · 2026Article
- Asynchronous Evolution of Epithelium and Stroma Differentiates Precursor Lesions from Pancreatic Cancer.Cancer discovery · 2026Article
- ResolVI: addressing noise and bias in spatial transcriptomics.Nature methods · 2026Article
- Spatial transcriptomics identifies a suppressive, T-cell-excluded tumor microenvironment in extramedullary myeloma.Blood advances · 2026Article
- Halo: a pretrained model for whole-cell segmentation from nuclei images in spatial transcriptomics.Briefings in bioinformatics · 2026Article
- Spatially guided in vivo single-cell functional genomics of postnatal heart.Nature cardiovascular research · 2026Article
- Aging-Related Changes in the Injury Response of the Peripheral Nervous System.Neuroscience bulletin · 2026Review
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
- Spatial transcriptomics in ovarian biology technologies: computational challenges, and biological insights.Reproduction (Cambridge, England) · 2026Review
- Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets.Nature biotechnology · 2026Article
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Review
- Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.Nature methods · 2026Article
- A spatial code governs olfactory receptor choice and aligns sensory maps in the nose and brain.Cell · 2026Article
- Mapping of Neutrophils in Cancers: Insights From Spatial Omics Technologies.European journal of immunology · 2026Review
- A transcriptomic-driven segmentation and cell simulation framework for high-resolution spatial transcriptomics and cell-cell communication.bioRxiv : the preprint server for biology · 2026Article
- Epstein-Barr virus orchestrates spatial reorganization and immunomodulation in the classic Hodgkin lymphoma tumor microenvironment.Cell reports. Medicine · 2026Article
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6 authors.
Funding
Abstract
Single-cell spatial transcriptomics promises a highly detailed view of a cell's transcriptional state and microenvironment, yet inaccurate cell segmentation can render these data murky by misattributing large numbers of transcripts to nearby cells or conjuring nonexistent cells. We adopt methods from ab initio cell simulation, in a method called Proseg (probabilistic segmentation), to rapidly infer morphologically plausible cell boundaries. Benchmarking applied to datasets generated by three commercial platforms shows superior performance and computational efficiency of Proseg when compared to existing methods. We show that improved accuracy in cell segmentation aids greatly in detection of difficult-to-segment tumor-infiltrating immune cells such as neutrophils and T cells. Last, through improvements in our ability to delineate subsets of tumor-infiltrating T cells, we show that CXCL13-expressing CD8
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.