ArticleNature communications2023
Virtual alignment of pathology image series for multi-gigapixel whole slide images.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
51 citing papers in PubMed.
- Patritumab deruxtecan in HRNature medicine · 2025Trial
- PASTA: versatile tyramide-oligonucleotide amplification for multimodal spatial biology.Nature methods · 2026Article
- Same-Slide Spatial Multiomics Integration with IN-DEPTH Reveals Tumor Virus-Linked Spatial Reorganization of the Tumor Microenvironment.Cancer discovery · 2026Article
- CurvReg: Curvature-aware registration for multi-stain alignment of liver biopsies.Journal of pathology informatics · 2026Article
- LYNX: a deep generative model for linking spatial dynamics and cell interactions in multimodal spatial data.bioRxiv : the preprint server for biology · 2026Article
- H&E-Referenced Multiplex Immunofluorescence Interpretation in TMA Cores: Spatial Co-localization, Cell Feature Validation, and Virtual H&E Generation.Research square · 2026Article
- Longitudinal evaluation of tumor-infiltrating lymphocyte scoring using automated region of interest registration in breast cancer.Breast cancer research : BCR · 2026Article
- Cross-Modality Alignment of Spatial Transcriptomics, Multiplexed Imaging, and Histology with PHARAOH.Research square · 2026Article
- Self-filtering monolithic organic/PbS quantum dot photodetector for visible and short-wave infrared selective vision in low-light.Nature communications · 2026Article
- Multifactorial sheltering in peristromal niches shapes in vivo responses of lung cancers to targeted therapies.Nature communications · 2026Article
- Joint zonated quantification of multiple parameters in hepatic lobules.Scientific reports · 2026Article
- SPOmiAlign: a modality-agnostic computational framework for multimodal spatial omics alignment enabled by a feature matching foundation model.Briefings in bioinformatics · 2026Article
- An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.Cell press blue · 2026Article
- Three-dimensional reconstruction of gigapixel whole-mount histopathology specimens with RAPID.Scientific reports · 2026Article
- Quantifying the Efficacy of Deep Learning-Driven Deformable Registration in Multiplexed-Immunofluorescence Imaging for Nucleus Subtype Classification.The journal of machine learning for biomedical imaging · 2026Article
- Generative AI for misalignment-resistant virtual staining to accelerate histopathology workflows.Nature communications · 2026Article
- Toward Computationally Complete Spatial Omics.bioRxiv : the preprint server for biology · 2026Article
- Mapping multipathology via spatial omic integration.Current opinion in biotechnology · 2026Review
- Minibeam radiation therapy remodels tumor microenvironment and suppresses HIF-1α/VEGFR axis to overcome radioresistance in triple-negative breast cancer.NPJ precision oncology · 2025Article
- µCodes: A Universal Grid Platform for Microscale Mapping, Microscopy Navigation, and Multimodal Imaging.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
Interest in spatial omics is on the rise, but generation of highly multiplexed images remains challenging, due to cost, expertise, methodical constraints, and access to technology. An alternative approach is to register collections of whole slide images (WSI), generating spatially aligned datasets. WSI registration is a two-part problem, the first being the alignment itself and the second the application of transformations to huge multi-gigapixel images. To address both challenges, we developed Virtual Alignment of pathoLogy Image Series (VALIS), software which enables generation of highly multiplexed images by aligning any number of brightfield and/or immunofluorescent WSI, the results of which can be saved in the ome.tiff format. Benchmarking using publicly available datasets indicates VALIS provides state-of-the-art accuracy in WSI registration and 3D reconstruction. Leveraging existing open-source software tools, VALIS is written in Python, providing a free, fast, scalable, robust, and easy-to-use pipeline for registering multi-gigapixel WSI, facilitating downstream spatial analyses.
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Registered trials
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.