ArticleeLife2019
Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 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.
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Who cites it
58 citing papers in PubMed.
- Development of the zebrafish foveal analogue: a quantitative atlas of high-acuity zone growth and retinal regionalisation.Biology open · 2026Article
- Whole-organ single-cell mapping defines growth dynamics and clonal organization in developing and adult zebrafish livers.PLoS biology · 2026Article
- Label-free 3D virtual histology of human formalin-fixed paraffin-embedded (FFPE) prostate needle biopsies with propagation-based phase-contrast micro-CT (PBCT).bioRxiv : the preprint server for biology · 2026Article
- Physics-driven deep learning photoacoustic tomography.Fundamental research · 2026Article
- Unlocking the hidden anatomy: synchrotron micro-tomography of the stomach, midgut, and organs in Penaeus vannamei and the potential route of Enterocytozoon hepatopaenaei (EHP) infection.Cell and tissue research · 2026Article
- Zebrafish gon4la mutants recapitulate human GON4L-related growth disorders and reveal novel metabolic organs abnormalities.Scientific reports · 2026Article
- Bioimaging of sense organs and the central nervous system in extant fishes and reptiles in situ: A review.Anatomical record (Hoboken, N.J. : 2007) · 2026Review
- Building a framework for reproducibility: the case for standardized data reporting and metadata integration in zebrafish research.Disease models & mechanisms · 2025Article
- Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive 3D Imaging of Whole Zebrafish Using a Water-Based Clearing Reagent for Hard Tissues.Zebrafish · 2025Article
- 3D multiscale characterization of the human placenta: Bridging anatomy and histology by X-ray phase-contrast tomography.PNAS nexus · 2025Article
- Co-option of neck muscles supported the vertebrate water-to-land transition.Nature communications · 2024Article
- Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach.Scientific reports · 2024Article
- 3D visualization and printing: An "Anatomical Engineering" trend revealing underlying morphology via innovation and reconstruction towards future of veterinary anatomy.Anatomical science international · 2024Review
- Novel Development of Magnetic Resonance Imaging to Quantify the Structural Anatomic Growth of Diverse Organs in Adult and Mutant Zebrafish.Zebrafish · 2024Article
- Article
- Recent Advances in Bioimage Analysis Methods for Detecting Skeletal Deformities in Biomedical and Aquaculture Fish Species.Biomolecules · 2023Review
- Sinogram domain angular upsampling of sparse-view micro-CT with dense residual hierarchical transformer and attention-weighted loss.Computer methods and programs in biomedicine · 2023Article
- Topological packing statistics of living and nonliving matter.Science advances · 2023Article
- Article
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Micro-CT optimized for cellular characterization (histotomography) allows brain nuclei to be computationally segmented and assigned to brain regions, and cell shapes and volumes to be computed for motor neurons and red blood cells. Striking individual phenotypic variation was apparent from color maps of computed densities of brain nuclei. Unlike histology, the histotomography also allows the study of 3-dimensional structures of millimeter scale that cross multiple tissue planes. We expect the computational and visual insights into 3D cell and tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.
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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.