Publications

Papers, chapters and preprints, newest first. Selected work at the top carries a one-line takeaway written by hand.

The authoritative list is ORCID 0000-0002-0332-4903; a Google Scholar profile is also kept current. Work by group members that I did not co-author is included. Where a paper produced code or a dataset, the entry links to it directly.

Selected work

Papers that between them describe what the group does and why.

2026
Single-exposure statistical retrieval of the directional dark-field signal
Kefs, Magnin, Brun et al. · Optica 13(6)

Orientation and anisotropy from one image pair, without assuming what the scattering profile looks like. This is the method behind SerPy.

code

2023
Shirani et al. · Nature communications

Cement setting watched in three dimensions as it happens, at the nanoscale — the same wave-optical toolbox, pointed at a material rather than a tissue.

2020
Pavlov et al. · Journal of Optics

Attenuation, phase and dark-field pulled from the same speckle images at once: the multi-channel picture the viewer on our home page illustrates.

2016
Brun et al. · Proceedings of the National Academy of Sciences

Lead found in the ink of the Herculaneum scrolls, overturning the assumption that ancient ink was carbon only — and explaining why the letters can be read at all.

Everything

107 entries, newest first. Datasets are listed separately under code and data.

2025

  1. A self-healing radiopaque hyaluronic acid hydrogel as a new injectable biomaterial for precision medicine in osteoarthritis. Said et al. · Theranostics
  2. How X-ray dark-field imaging relates to small-angle X-ray scattering measurements. Magnin et al. · Journal of applied crystallography
  3. Longitudinal imaging with multicolour CT provides a surrogate marker of response to treatment with a novel iodine-labelled hydrogel in a murine model of osteoarthritis — · conference paper
  4. Review and experimental comparison of speckle-tracking algorithms for X-ray phase contrast imaging Celestre et al. · Journal of Synchrotron Radiation
  5. Twelve Years of LabEx PRIMES (2012-2024) — · book

2024

  1. 3D quantification of the lacunocanalicular network on human femoral diaphysis through synchrotron radiation-based nanoCT Yu et al. · Journal of Structural Biology
  2. Combining Wave and Particle Effects in the Simulation of X-ray Phase Contrast—A Review Pietersoone et al. · Instruments
  3. In vivo monitoring of stem cells and their encapsulating scaffold using dual-contrast agent labelling and multicolour CT: application in a murine model of osteoarthritis — · conference paper
  4. Refraction simulation for optimisation of X-Ray Phase Contrast imaging — · conference paper

2023

  1. 4D nanoimaging of early age cement hydration. Shirani et al. · Nature communications
  2. A novel injectable radiopaque hydrogel with potent properties for multicolor CT imaging in the context of brain and cartilage regenerative therapy Said et al. · — · preprint
  3. DISPOSITIF D'IMAGERIE, APPAREIL D'IMAGERIE OU DE CARACTERISATION DE MATERIAUX LE COMPRENANT ET PROCEDE D'IMAGERIE — · patent
  4. Dark-field and directional dark-field on low-coherence x ray sources with random mask modulations: validation with SAXS anisotropy measurements Magnin et al. · Optics Letters
  5. High-resolution synchrotron K-edge subtraction CT allows tracking and quantifying therapeutic cells and their scaffold in a rat model of focal cerebral injury and can serve as a reference for spectral photon counting CT. Tavakoli et al. · Nanotheranostics
  6. Human femoral lacuno-canalicular network by X-ray nano-CT — · conference paper
  7. Human fetal virtual histology with X-ray phase contrast imaging Vérot et al. · — · preprint
  8. Imagerie cutanée par rayonnement synchrotron : application aux pseudo-engelures COVID-19 Mouret et al. · — · conference paper
  9. In vivo monitoring of hydrogel-embedded stem cells: combination of Synchrotron X-ray phase-contrast and multi-spectral imaging applied to osteoarthritis mice models. — · conference paper
  10. In vivo targeting and multimodal imaging of cerebral amyloid-β aggregates using hybrid GdF 3 nanoparticles Lerouge et al. · Nanomedicine
  11. Quantification of cartilage and subchondral bone cysts on knee specimens based on a spectral photon-counting computed tomography Garcelon et al. · Scientific Reports
  12. Taking into account wave effects in Monte Carlo simulation of phase contrast imaging using the Wigner Distribution Function Pietersoone et al. · — · conference paper
  13. Use of metal-based contrast agents for in vivo MR and CT imaging of phagocytic cells in neurological pathologies Wiart et al. · Journal of Neuroscience Methods
  14. Virtual histology of Alzheimer's disease: Biometal entrapment within amyloid-β plaques allows for detection via X-ray phase-contrast imaging. Chourrout et al. · Acta biomaterialia

2022

  1. Brain virtual histology with X-ray phase-contrast tomography Part I: whole-brain myelin mapping in white-matter injury models Chourrout et al. · Biomedical Optics Express · newspaper article
  2. Brain virtual histology with X-ray phase-contrast tomography Part II: 3D morphologies of amyloid-β plaques in Alzheimer’s disease models Chourrout et al. · Biomedical Optics Express · newspaper article
  3. Evaluating inflammations in high-resolution x-ray phase contrast images of SKG spondylarthritis mice models Singh et al. · Developments in X-Ray Tomography XIV · conference paper
  4. In Vitro Preparation of Actively Maturing Bovine Articular Cartilage Explants for X-Ray Phase Contrast Imaging Bissardon et al. · Journal of Visualized Experiments · newspaper article
  5. Monitoring the fate of stem cells and encapsulating hydrogel intraarticularly injected in mice knees using Synchrotron K-edge subtraction computed tomography — · conference paper
  6. Monitoring the fate of stem cells and their encapsulating hydrogel in mice knees using Synchrotron K-edge subtraction computed tomography — · conference paper
  7. Mouse Models of Osteoarthritis: A Summary of Models and Outcomes Assessment. Drevet et al. · Comparative medicine
  8. New imaging tools for mouse models of osteoarthritis Drevet et al. · GeroScience
  9. Virtual monoenergetic images from photon-counting spectral computed tomography to assess knee osteoarthritis Chappard et al. · European Radiology Experimental
  10. X-ray Phase Contrast Imaging from Synchrotron to Conventional Sources: A Review of the Existing Techniques for Biological Applications Quenot et al. · Applied Sciences

2021

  1. An iodine-labelled hyaluronic acid-based hydrogel : a radiopaque biopolymer to monitor the fate of bioscaffold in cell therapy applications — · conference paper
  2. Bicolor imaging to track therapeutic cells and their encapsulating scaffold: translation from synchrotron to spectral photon counting computed tomography — · conference paper
  3. Calcified cartilage revealed in whole joint by X-ray phase contrast imaging Broche et al. · Osteoarthritis and Cartilage Open
  4. Contributions à l’Imagerie Synchrotron : Applications et Transfert sur Sources Conventionnelles — · dissertation thesis
  5. Directional dark-field implicit x-ray speckle tracking using an anisotropic-diffusion Fokker-Planck equation Pavlov et al. · Physical Review A
  6. Evaluation of simulators for x-ray speckle-based phase contrast imaging Quénot et al. · Physics in Medicine & Biology
  7. Imagerie en contraste de phase par source synchrotron appliquée à l’étude anatomique de la vascularisation de la main Cruz et al. · Morphologie
  8. Implicit tracking approach for X-ray phase-contrast imaging with a random mask and a conventional system Quénot et al. · Optica
  9. Lattice kinetic model of 3D flow characterization in core samples via synchrotron X-ray micro-tomography Kakouie et al. · Computers & Geosciences
  10. Multimodal Imaging with NanoGd Reveals Spatiotemporal Features of Neuroinflammation after Experimental Stroke Hubert et al. · Advanced Science
  11. Synchrotron phase-contrast imaging applied to the anatomical study of the hand and its vascularization Solé Cruz et al. · Journal of Anatomy
  12. Towards x-ray phase contrast tomography in clinical conditions: simulation and phase retrieval development Quénot et al. · Medical Imaging 2021: Physics of Medical Imaging · conference paper
  13. Tracking cells in the brain of small animals using synchrotron multi-spectral phase contrast imaging Tavakoli et al. · Medical Imaging 2021: Physics of Medical Imaging · conference paper

2019

  1. 3D histopathology speckle phase contrast imaging: From synchrotron to conventional sources Labriet et al. · Progress in Biomedical Optics and Imaging - Proceedings of SPIE · conference paper
  2. Single-shot x-ray speckle-based imaging of a single-material object Pavlov et al. · — · preprint

2018

  1. Dosimetry for synchrotron imaging techniques — · conference paper
  2. Quantitative Assessment of Degenerative Cartilage and Subchondral Bony Lesions in a Preserved Cadaveric Knee: Propagation-Based Phase-Contrast CT Versus Conventional MRI and CT. Geith et al. · AJR. American journal of roentgenology
  3. Significant dose reduction using synchrotron radiation computed tomography: first clinical case and application to high resolution CT exams. Labriet et al. · Scientific reports
  4. Single-image geometric-flow x-ray speckle tracking Paganin et al. · Physical Review A
  5. Virtual histology of animal and human brains with Alzheimer's disease — · conference paper

2015

  1. A single-image method for x-ray refractive index CT Mittone et al. · Physics in Medicine and Biology
  2. High contrast microstructural visualization of natural acellular matrices by means of phase-based x-ray tomography Hagen et al. · Sci. Rep.
  3. Microstructure of out-of-pile annealed neutron irradiated beryllium studied by X-ray tomography Vladimirov et al. · Acta Materialia
  4. Pebble bed structures in the vicinity of concave and convex walls Reimann et al. · Fusion Engineering and Design
  5. Revealing letters in rolled Herculaneum papyri by X-ray phase-contrast imaging Mocella, Brun, Ferrero & Delattre · Nat Comms
  6. Single-image phase retrieval using an edge illumination X-ray phase-contrast imaging setup Diemoz et al. · J Synchrotron Radiat
  7. Synchrotron X-ray boost delivered by Microbeam Radiation Therapy improves glioma control after conventional fractionated X-ray therapy — · conference paper

2014

  1. A dictionary learning approach with overlap for the low dose computed tomography reconstruction and its vectorial application to differential phase tomography Mirone et al. · PLoS ONE
  2. Breast tumor segmentation in high resolution x-ray phase contrast analyzer based computed tomography Brun et al. · Medical Physics
  3. Cartilage and soft tissue imaging using X-rays: Propagation-based phase-contrast computed tomography of the Human Knee in comparison with clinical imaging techniques and histology Horng et al. · Investigative Radiology
  4. PyHST2: an hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms
  5. The PyHST2 hybrid distributed code for high speed tomographic reconstruction with iterative reconstruction and a priori knowledge capabilities Mirone et al. · Nuclear Instruments and Methods in Physics Research, Section B: Beam Interactions with Materials and Atoms
  6. Tomographic reconstruction of the refractive index with hard X-rays: An efficient method based on the gradient vector-field approach Gasilov et al. · Optics Express

2011

  1. Imaging of the angular-dependent coherent-scatter cross section with analyzer crystal: A Monte Carlo simulation Optics Letters
  2. SU‐E‐I‐144: Radiation Dose Reduction in Monochromatic Phase Contrast X‐Ray Mammography Using Equally Sloped Tomography Zhao et al. · Medical Physics

2010

  1. Conjugate heat and mass transfer in metal foams: A numerical study for heat exchangers design Hugo et al. · Defect and Diffusion Forum
  2. From pore scale numerical simulation of conjugate heat transfer in cellular material to effectives transport properties of real structures Hugo et al. · 2010 14th International Heat Transfer Conference, IHTC 14 · conference paper
  3. Volumetric segmentation of trabecular bone into rods and plates: A new method based on local shape classification Brun et al. · Progress in Biomedical Optics and Imaging - Proceedings of SPIE · conference paper

2008

  1. Characterization of the full thermal conductivity tensor of anisotropic metal foams - influence of the fluid phase MetFoam 2007 - Proceedings of the 5th International Conference on Porous Metals and Metallic Foams · conference paper
  2. FROM 3D IMAGING OF STRUCTURES TO DIFFUSIVE PROPERTIES OF ANISOTROPIC CELLULAR MATERIALS — · conference paper
  3. Geometrical measurement of real foams from 3D images MetFoam 2007 - Proceedings of the 5th International Conference on Porous Metals and Metallic Foams · conference paper

2007

  1. Restoration of variable area soundtracks Brun et al. · Proceedings - International Conference on Image Processing, ICIP · conference paper