ReviewNature protocols2023
Preparation of large biological samples for high-resolution, hierarchical, synchrotron phase-contrast tomography with multimodal imaging compatibility.
Review in Nature protocols, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 46 citations in OpenAlex.
- Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys.Nature communications · 2026Pooled it
- Evolution of hierarchical phase-contrast tomography on the European Synchrotron beamlines BM05 and BM18: a whole adult human brain imaging case study.Journal of synchrotron radiation · 2026Article
- Advancing three-dimensional tendon imaging using laboratory X-ray phase contrast techniques and refined sample preparation.Scientific reports · 2026Article
- The heterogeneous nature of atrioventricular conduction tissues in tetralogy of Fallot demonstrated by hierarchical phase-contrast tomography.JTCVS structural and endovascular · 2026Article
- The pleuroparenchymal fibroelastosis atlas reveals aberrant cell states and their zonation as an alternate roadmap to lung fibrosis.Science advances · 2026Article
- Multimodal techniques based on synchrotron radiation X-rays for revealing interactions of metallic nanoparticles with biological matrices.Fundamental research · 2026Review
- Bridging the microstructural gap in human connectomics using hierarchical phase-contrast tomography as a reference for diffusion MRI in the human brain.bioRxiv : the preprint server for biology · 2026Article
- The Human Organ Atlas.Science advances · 2026Article
- [Virtual histopathology of the pancreas: 3D insights using synchrotron-based imaging].Pathologie (Heidelberg, Germany) · 2026Article
- The Extremely Brilliant Brain: An Isotropic Microscale Human Brain Dataset.bioRxiv : the preprint server for biology · 2026Article
- Multiscale segmentation using hierarchical phase-contrast tomography and deep learning.PLoS computational biology · 2026Article
- Mapping the arterial vascular network in an intact human kidney using hierarchical phase-contrast tomography.Npj imaging · 2025Article
- Eikonal Phase Retrieval: unleashing the potential of fourth-generation sources for enhanced propagation-based tomography on biological samples.Journal of synchrotron radiation · 2025Article
- The Human Organ Atlas.bioRxiv : the preprint server for biology · 2025Article
- Synchrotron Radiation-Based Tomography of an Entire Mouse Brain with Sub-Micron Voxels: Augmenting Interactive Brain Atlases with Terabyte Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Air artifact suppression in phase contrast micro-CT using conditional generative adversarial networks.Journal of synchrotron radiation · 2025Article
- 3D multiscale characterization of the human placenta: Bridging anatomy and histology by X-ray phase-contrast tomography.PNAS nexus · 2025Article
- Deep learning for 3D vascular segmentation in hierarchical phase contrast tomography: a case study on kidney.Scientific reports · 2024Article
- Micro to macro scale anatomical analysis of the human hippocampal arteries with synchrotron hierarchical phase-contrast tomography.Surgical and radiologic anatomy : SRA · 2024Article
Corrections and comments
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Authors and funding
11 authors at 9 institutions in 4 countries.
Funding
Abstract
Imaging across different scales is essential for understanding healthy organ morphology and pathophysiological changes. The macro- and microscale three-dimensional morphology of large samples, including intact human organs, is possible with X-ray microtomography (using laboratory or synchrotron sources). Preparation of large samples for high-resolution imaging, however, is challenging due to limitations such as sample shrinkage, insufficient contrast, movement of the sample and bubble formation during mounting or scanning. Here, we describe the preparation, stabilization, dehydration and mounting of large soft-tissue samples for X-ray microtomography. We detail the protocol applied to whole human organs and hierarchical phase-contrast tomography at the European Synchrotron Radiation Facility, yet it is applicable to a range of biological samples, including complete organisms. The protocol enhances the contrast when using X-ray imaging, while preventing sample motion during the scan, even with different sample orientations. Bubbles trapped during mounting and those formed during scanning (in the case of synchrotron X-ray imaging) are mitigated by multiple degassing steps. The sample preparation is also compatible with magnetic resonance imaging, computed tomography and histological observation. The sample preparation and mounting require 24-36 d for a large organ such as a whole human brain or heart. The preparation time varies depending on the composition, size and fragility of the tissue. Use of the protocol enables scanning of intact organs with a diameter of 150 mm with a local voxel size of 1 μm. The protocol requires users with expertise in handling human or animal organs, laboratory operation and X-ray imaging.
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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.