Paul Tafforeau

• PhD
• Project Manager at European Synchrotron Radiation Facility

Studying the subtle and intricate three-dimensional structure of the human cochlea embedded in the temporal bone requires structure-preserving imaging approaches with adaptable field of view and resolution. Synchrotron X-ray phase-contrast tomography at the novel beamline BM18 (EBS, ESRF) offers the unique capability to achieve histological resolut...

A bstract Biomedical systems span multiple spatial scales, encompassing tiny functional units to entire organs. Interpreting these systems through image segmentation requires the effective propagation and integration of information across different scales. However, most existing segmentation methods are optimised for single-scale imaging modalities...

Background Fibrotic lung disease is a progressive illness that causes scarring and ultimately respiratory failure, with irreversible damage by the time it is diagnosed on computed tomography imaging. Recent research postulates the role of the lung vasculature on the pathogenesis of the disease. With the recent development of high-resolution hierarc...

The human placenta exhibits a complex three dimensional (3D) structure with a complex interpenetrating vascular tree and large internal interfacial area. In a unique and yet insufficiently explored way, this parenchymal structure enables its multiple functions as a respiratory, renal, and gastrointestinal multiorgan. The histopathological states ar...

Human life history is characterized by an extended period of immaturity during which there is a disjunction between cerebral and somatic growth rates¹. This mode of ontogeny is thought to be essential for the acquisition of advanced cognitive capabilities in a socially complex environment while the brain is still growing². Key information about whe...

Automated blood vessel segmentation is critical for biomedical image analysis, as vessel morphology changes are associated with numerous pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. Our...

Ankylosaurs were a group of heavily armored non‐avian dinosaurs (Dinosauria, Ankylosauria), represented by a relatively abundant fossil record from the Cretaceous of North and South America. Their dermal skeleton was characterized by large osteoderms whose development and functional role have been largely investigated. However, interstitial small o...

Transparent crystalline scintillators such as cerium-doped YAG or LuAG are widely used in X-ray imaging for the indirect detection of X-rays. The application of reflective coatings on the front side to improve the optical gain is common practice for flat panel detectors with CsI or Gd2O2S powder scintillators but still largely unknown for crystalli...

Purpose To date, no non-invasive imaging modality has been employed to profile the structural intricacies of the hippocampal arterial microvasculature in humans. We hypothesised that synchrotron-based imaging of the human hippocampus would enable precise characterisation of the arterial microvasculature. Methods Two preserved human brains from, a...

Efficient algorithms are needed to segment vasculature in new three-dimensional (3D) medical imaging datasets at scale for a wide range of research and clinical applications. Manual segmentation of vessels in images is time-consuming and expensive. Computational approaches are more scalable but have limitations in accuracy. We organized a global ma...

Purpose To date, no non-invasive imaging modality has been employed to profile the structural intricacies of the hippocampal arterial microvasculature in humans. We hypothesised that synchrotron-based imaging of the human hippocampus would enable precise characterisation of the arterial microvasculature. Methods Two preserved human brains from, a...

Automated blood vessel segmentation is critical for biomedical image analysis, as vessel morphology changes are associated with numerous pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. Our...

Background Current clinical imaging modalities such as CT and MRI provide resolution adequate to diagnose cardiovascular diseases but cannot depict detailed structural features in the heart across length scales. Hierarchical phase-contrast tomography (HiP-CT) uses fourth-generation synchrotron sources with improved x-ray brilliance and high energie...

The evolution of synchrotrons towards higher brilliance beams has increased the possible sample-to-detector propagation distances for which the source confusion circle does not lead to geometrical blurring. This makes it possible to push near-field propagation driven phase contrast enhancement to the limit, revealing low contrast features which wou...

The evolution of synchrotrons towards higher brilliance beams has increased the possible sample-to-detector propagation distances for which the source confusion circle does not lead to geometrical blurring. This makes it possible to push near-field propagation driven phase contrast enhancement to the limit, revealing low contrast features which wou...

Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image qual...

Cardiovascular diseases (CVDs) are a leading cause of death worldwide. Current clinical imaging modalities provide resolution adequate for diagnosis but are unable to provide detail of structural changes in the heart, across length-scales, necessary for understanding underlying pathophysiology of disease. Hierarchical Phase-Contrast Tomography (HiP...

Acoustic communication involves two processes in Anurans: sending signals and receiving them [1]. The signal sent changes due to environmental parameters and differs from the signal received. Yet, calling frogs hear in a wide range of habitats, in open or closed, absorbent or noisy environments [2]. In these conditions, frogs have adapted to their...

The peopling of the Americas and human interaction with the Pleistocene megafauna in South America remain hotly debated. The Santa Elina rock shelter in Central Brazil shows evidence of successive human settlements from around the last glacial maximum (LGM) to the Early Holocene. Two Pleisto-cene archaeological layers include rich lithic industry a...

The peopling of the Americas and human interaction with the Pleistocene megafauna in South America remain hotly debated. The Santa Elina rock shelter in Central Brazil shows evidence of successive human settlements from around the last glacial maximum (LGM) to the Early Holocene. Two Pleistocene archaeological layers include rich lithic industry as...

The peopling of the Americas and human interaction with the Pleistocene megafauna in South America remain hotly debated. The Santa Elina rock shelter in Central Brazil shows evidence of successive human settlements from around the last glacial maximum (LGM) to the Early Holocene. Two Pleistocene archaeological layers include rich lithic industry as...

Recent excavations in the Rising Star Cave System of South Africa have revealed burials of the extinct hominin species Homo naledi. A combination of geological and anatomical evidence shows that hominins dug holes that disrupted the subsurface stratigraphy and interred the remains of H. naledi individuals, resulting in at least two discrete feature...

Recent excavations in the Rising Star Cave System of South Africa have revealed burials of the extinct hominin species Homo naledi. A combination of geological and anatomical evidence shows that hominins dug holes that disrupted the subsurface stratigraphy and interred the remains of H. naledi individuals, resulting in at least two discrete feature...

Recent excavations in the Rising Star Cave System of South Africa have revealed burials of the extinct hominin species Homo naledi. A combination of geological and anatomical evidence shows that hominins dug holes that disrupted the subsurface stratigraphy and interred the remains of H. naledi individuals, resulting in at least two discrete feature...

Jensen et al. (1) question evidence presented of a chambered heart within placoderms, citing its small size and apparently ventral atrium. However, they fail to note the belly-up orientation of the placoderm within one nodule, and the variability of heart morphology within extant taxa. Thus, we remain confident in our interpretation of the minerali...

Background: The kidney vasculature is exquisitely structured to orchestrate renal function. Structural profiling of the vasculature in intact rodent kidneys, has provided insights into renal haemodynamics and oxygenation, but has never been extended to the human kidney beyond a few vascular generations. We hypothesised that synchrotron-based imagin...

Detailed histological analyses are desirable for zebrafish mutants that are models for human skeletal diseases, but traditional histological techniques are limited to two-dimensional thin sections with orientations highly dependent on careful sample preparation. On the other hand, techniques that provide three-dimensional (3D) datasets including µC...

Synchrotron phase-contrast micro-tomography is considered the gold standard in non-destructive volumetric imaging of millimeter and centimeter-sized objects. Micro-tomography beamlines are operating at many synchrotron radiation facilities, including the Extremely Brilliant Source (EBS) at the European Synchrotron Radiation Facility (ESRF). Applica...

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-resolu...

Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image qual...

An improved understanding of an ovary’s structures is highly desirable to support advances in folliculogenesis knowledge and reproductive medicine, with particular attention to fertility preservation options for prepubertal girls with malignant tumors. Although currently the golden standard for structural analysis is provided by combining histologi...

Giant anuran species express a morphology with hyper ossification, a large head (which impacts the distance between the inner and outer ear), and a larynx that may be as long as the head as, for example, in Pipa pipa. There is currently no theoretical model that can explain the variety of changes in form and function observed with increasing size....

The ESRF tomography software is undergoing a major re-write, targeted at unifying the tomography user experience, data acquisition, data format, and processing tools. To cope with the inherent large complexity of handling data coming from multiple beamlines, techniques and facilities, we are developing an open source software called NXtomomill . It...

Background COVID-19 is characterized by a heterogeneous clinical presentation, ranging from mild symptoms to severe courses of disease. 9–20% of hospitalized patients with severe lung disease die from COVID-19 and a substantial number of survivors develop long-COVID. Our objective was to provide comprehensive insights into the pathophysiology of se...

The origin and early diversification of jawed vertebrates involved major changes to skeletal and soft anatomy. Skeletal transformations can be examined directly by studying fossil stem gnathostomes; however, preservation of soft anatomy is rare. We describe the only known example of a three-dimensionally mineralized heart, thick-walled stomach, and...

Objet L’hippocampe est une structure cérébrale temporale appartenant au lobe limbique, impliquée dans de nombreux processus physiopathologiques. L’amélioration de la connaissance de la vascularisation de l’hippocampe pourrait permettre d’améliorer les thérapeutiques. L’imagerie en contraste de phase par source synchrotron (sPCI) permet d’étudier pr...

Objet L’architecture capillaire et la circulation bronchique habituelle semble sensiblement modifiée dans le cadre des pneumopathies à SARS-CoV-2, associés à des thromboses multiples [1], [2]. L’imagerie en contraste de phase par source synchrotron (sPCI) permet d’étudier précisément l’ensemble des tissus organiques à une résolution microscopique e...

Snakes comprise nearly 4,000 extant species found on all major continents except Antarctica. Morphologically and ecologically diverse, they include burrowing, arboreal, and marine forms, feeding on prey ranging from insects to large mammals. Snakes are strikingly different from their closest lizard relatives, and their origins and early diversifica...

Imaging the different scales of biological tissue is essential for understanding healthy organ behavior and pathophysiological changes. X-ray micro-tomography using both laboratory (μCT) and synchrotron sources (sCT) is a promising tool to image the 3D morphology at the macro- and micro-scale of large samples, including intact human organs. Prepara...

Technological advancements in X-ray imaging using bright and coherent synchrotron sources now allows the decoupling of sample size and resolution while maintaining high sensitivity to the microstructures of soft, partially dehydrated tissues. The continuous developments in multiscale X-ray imaging resulted in hierarchical phase-contrast tomography,...

The ESRF tomography software is undergoing a complete rewrite, targeted at unifying the tomography user experience, acquisition, data format, and processing tools. NXtomomill plays a key role in managing the large complexity of the data coming from multiple beamlines, techniques and facilities, by offering advanced data conversion, manipulation and...

The Cretaceous–Palaeogene mass extinction around 66 million years ago was triggered by the Chicxulub asteroid impact on the present-day Yucatán Peninsula1,2. This event caused the highly selective extinction that eliminated about 76% of species3,4, including all non-avian dinosaurs, pterosaurs, ammonites, rudists and most marine reptiles. The timin...

Propagation Phase Contrast Synchrotron Microtomography (PPC-SRμCT) is the gold standard for non-invasive and non-destructive access to internal structures of archaeological remains. In this analysis, the virtual specimen needs to be segmented to separate different parts or materials, a process that normally requires considerable human effort. In th...

Technological advancements in X-ray imaging using bright and coherent synchrotron sources now allows to decouple sample size and resolution, while maintaining high sensitivity to the microstructure of soft, partially dehydrated tissues. The recently developed imaging technique, hierarchical phase-contrast tomography, is a comprehensive approach to...

Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)’s Extremely Brilliant Source (EBS). The spatial cohe...

The Cretaceous-Paleogene (KPg) mass extinction ~66 million years ago (Ma) was triggered by the Chicxulub impact on the present-day Yucatán Peninsula. This event caused the extinction of circa 76% of species, including all non-avian dinosaurs, and represents one of the most selective extinctions to date. The timing of the impact and its aftermath ha...

Propagation Phase Contrast Synchrotron Microtomography (PPC-SR${\mu}$CT) is the gold standard for non-invasive and non-destructive access to internal structures of archaeological remains. In this analysis, the virtual specimen needs to be segmented to separate different parts or materials, a process that normally requires considerable human effort....

Brain evolution in early Homo Human brains are larger than and structurally different from the brains of the great apes. Ponce de León et al. explored the timing of the origins of the structurally modern human brain (see the Perspective by Beaudet). By comparing endocasts, representations of the inner surface of fossil brain cases, from early Homo...

The production of blood cells (haematopoiesis) occurs in the limb bones of most tetrapods but is absent in the fin bones of ray-finned fish. When did long bones start producing blood cells? Recent hypotheses suggested that haematopoiesis migrated into long bones prior to the water-to-land transition and protected newly-produced blood cells from har...

The ESRF tomography acquisition and processing software's fragmentation across the different beamlines resulted in high maintenance and development costs, which have severely hindered its progress. We are currently rethinking the acquisition and processing workflows from scratch, to deliver a unified solution to the tomography beamlines. This will...

Human organs are complex, three-dimensional and multiscale systems. Spatially mapping the human body down through its hierarchy, from entire organs to their individual functional units and specialised cells, is a major obstacle to fully understanding health and disease. To meet this challenge, we developed hierarchical phase-contrast tomography (Hi...

The discovery of a new fossil species of the Caribbeo-Mexican genus Proptomaphaginus (Coleoptera, Leiodidae, Cholevinae) from Dominican amber, associated with a new fossil parasitic fungus in the genus Columnomyces (Ascomycota, Laboulbeniales), triggered an investigation of extant species of Proptomaphaginus and revealed the long-enduring parasitic...

The anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups—holocephalans and elasmobranchs—have played a...

We are redesigning the ESRF tomography software for both data acquisition and processing, to offer unified user experience, data format and processing software across all beamlines. This will foster collaborations with the leading research groups in the field.

The ontogenetic trajectory of a marginal jawbone of Lophosteus superbus (Late Silurian, 422 Million years old), the phylogenetically most basal stem osteichthyan, visualized by synchrotron microtomography, reveals a developmental relationship between teeth and dermal odontodes that is not evident from the adult morphology. The earliest odontodes ar...

Growth plate and articular cartilage constitute a single anatomical entity early in development but later separate into two distinct structures by the secondary ossification center (SOC). The reason for such separation remains unknown. We found that evolutionarily SOC appears in animals conquering the land - amniotes. Analysis of the ossification p...

Growth plate and articular cartilage constitute a single anatomical entity early in development but later separate into two distinct structures by the secondary ossification center (SOC). The reason for such separation remains unknown. We found that evolutionarily SOC appears in animals conquering the land - amniotes. Analysis of the ossification p...

Despite considerable advances in knowledge of the anatomy, ecology and evolution of early mammals, far less is known about their physiology. Evidence is contradictory concerning the timing and fossil groups in which mammalian endothermy arose. To determine the state of metabolic evolution in two of the earliest stem-mammals, the Early Jurassic Morg...

Growth plate and articular cartilage constitute a single anatomical entity early in development, but later separate into two distinct structures by the secondary ossification center (SOC). The reason for such separation remains unknown. We found that evolutionarily SOC appears in animals conquering the land - amniotes. Analysis of ossification patt...

The anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates, due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups - holocephalans and elasmobranchs - have pla...

Ontogenetic data obtained by synchrotron microtomography of a marginal jawbone of Lophosteus superbus (Late Silurian, 422 Million years old), the phylogenetically basalmost stem osteichthyan, reveal developmental relationships between teeth and ornament that are not obvious from the adult morphology. The earliest odontodes are two longitudinal foun...

Teeth and jaws The first vertebrates were jawless, much like a modern hagfish. There has been a lot of interest in how these forms transitioned to having jaws like most of their descendants, including humans. Much of our understanding of this process has focused on how the teeth are replaced relative to the jaw. Previous theories suggested that too...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The ontogeny of the paired appendages has been extensively studied in lungfishes and tetrapods, but remains poorly known in coelacanths. Recent work has shed light on the anatomy and development of the pectoral fin in Latimeria chalumnae. Yet, information on the development of the pelvic fin and girdle is still lacking. Here, we described the devel...

Tetrapod life on land was the result of a lengthy process, the final steps of which resulted in full independence of amniotic tetrapods from the aquatic environment. Developmental strategies, including growth rate and the attainment of sexual maturity, played a major role in this transition. Early amniotes, such as Ophiacodon, tended to reach sexua...

Human brains are three times larger, are organized differently, and mature for a longer period of time than those of our closest living relatives, the chimpanzees. Together, these characteristics are important for human cognition and social behavior, but their evolutionary origins remain unclear. To study brain growth and organization in the homini...