ArticleNature methods2022
CODA: quantitative 3D reconstruction of large tissues at cellular resolution.
Article in Nature methods, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
118 citing papers in PubMed, 163 citations in OpenAlex.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Article
- Molecular programs in human locus coeruleus link APOE and neuromelanin to Alzheimer's vulnerability.Acta neuropathologica · 2026Article
- Review
- Deep-learning triage of three-dimensional pathology datasets for comprehensive and efficient pathologist assessments.Nature biomedical engineering · 2026Article
- Deep learning-driven 3-D histopathology method: a pipeline for cellular-resolution myocarditis analysis.American journal of physiology. Heart and circulatory physiology · 2026Article
- Deep learning-powered quantification of endocrine cells and CD3Diabetologia · 2026Article
- Tissue and cellular spatiotemporal dynamics in colon aging.Nature biotechnology · 2026Article
- Real-time single-particle imaging of functional lungs reveals mosaic-like patterns of aerosol deposition in alveoli.Nature biomedical engineering · 2026Article
- CODAvision: best practices and a user-friendly interface for rapid, customizable segmentation of medical images.Nature protocols · 2026Review
- High-precision label-free virtual H&E staining of 3D holotomography using DAPI-guided conditional diffusion learning.International journal of computer assisted radiology and surgery · 2026Article
- Rapid autofluorescence based 3D optical imaging of the pancreatic cancer milieu at mesoscopic scale - stain-free volumetric segmentation.Scientific reports · 2026Article
- Volumetric Cyclic Immunofluorescence for 3D Spatial Profiling of Immune Structures in Human FFPE Tissue.bioRxiv : the preprint server for biology · 2026Article
- Quantitative 3D histology reveals localized immune remodeling during early pancreatic cancer progression.Cell press blue · 2026Article
- SPOmiAlign: a modality-agnostic computational framework for multimodal spatial omics alignment enabled by a feature matching foundation model.Briefings in bioinformatics · 2026Article
- Morphological abnormalities in the ureter of type XVII collagen-deficient mice.Scientific reports · 2026Article
- Virtual multiplex staining of the pancreatic islets across type 1 diabetes progression using a Schrödinger bridge.bioRxiv : the preprint server for biology · 2026Article
- Whole organism 3D mapping reveals universal branching topology and biophysical optimization governs vascular and nervous system development.bioRxiv : the preprint server for biology · 2026Article
- Three-dimensional reconstruction of gigapixel whole-mount histopathology specimens with RAPID.Scientific reports · 2026Article
- Multimodal spatial alignment and morphology mapping with MOSAICField.bioRxiv : the preprint server for biology · 2026Article
58 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors at 3 institutions in 2 countries.
Funding
Abstract
A central challenge in biology is obtaining high-content, high-resolution information while analyzing tissue samples at volumes relevant to disease progression. We address this here with CODA, a method to reconstruct exceptionally large (up to multicentimeter cubed) tissues at subcellular resolution using serially sectioned hematoxylin and eosin-stained tissue sections. Here we demonstrate CODA's ability to reconstruct three-dimensional (3D) distinct microanatomical structures in pancreas, skin, lung and liver tissues. CODA allows creation of readily quantifiable tissue volumes amenable to biological research. As a testbed, we assess the microanatomy of the human pancreas during tumorigenesis within the branching pancreatic ductal system, labeling ten distinct structures to examine heterogeneity and structural transformation during neoplastic progression. We show that pancreatic precancerous lesions develop into distinct 3D morphological phenotypes and that pancreatic cancer tends to spread far from the bulk tumor along collagen fibers that are highly aligned to the 3D curves of ductal, lobular, vascular and neural structures. Thus, CODA establishes a means to transform broadly the structural study of human diseases through exploration of exhaustively labeled 3D microarchitecture.
Indexed as
Identifiers
What OpenQuestion holds
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.