Paul Tafforeau

European Synchrotron Radiation Facility | ESRF · Division of Experiments

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...

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...

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...

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...

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...

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...

Ants exhibit a plethora of ecological interactions with terrestrial plants. These interactions are broadly surveyed in modern ecosystems, but are much more difficult to unveil in the fossil record. Here, we report a unique ant–conifer association preserved in an opaque piece of 100‐million‐year‐old amber from Charentes in Western France, revealed b...

Although Ancient Egyptians mummified millions of animals over the course of one millennium, many details of these mummification protocols remain unknown. Multi-scale propagation phase-contrast X-ray synchrotron microtomography was used to visualise an ancient Egyptian crocodile mummy housed at the Musée des Confluences (Lyon, France). This state-of...

One of the key issues to be resolved to improve the performance of silicon solar cells is to reduce crystalline defect formation and propagation during the growth-process fabrication step. For this purpose, the generation of structural defects such as grain boundaries and dislocations in silicon must be understood and characterized. Here, in situ X...

The ferrierite crystal structure has often been subject to discussion because of the possible lowering of symmetry from the space group Immm . It mainly occurs in nature with a fibrous crystal habit, and because of the existence of line/planar defects in the framework, texture and preferred orientation effects it has been difficult to obtain an exa...

The monobasal pectoral fins of living coelacanths and lungfishes are homologous to the forelimbs of tetrapods and are thus critical to investigate the origin thereof. However, it remains unclear whether the similarity in the asymmetrical endoskeletal arrangement of the pectoral fins of coelacanths reflects the evolution of the pectoral appendages i...

In the last few decades, hook‐like structures have been reported in the Mesozoic ammonite family Scaphitidae. Despite their exceptional preservation and debates about their function, no detailed reconstruction has been available until now. For the first time, we describe the composition and details of the morphology of these structures found in the...

There is uncertainty regarding the timing and fossil species in which mammalian endothermy arose, with few studies of stem-mammals on key aspects of endothermy such as basal or maximum metabolic rates, or placing them in the context of living vertebrate metabolic ranges. Synchrotron X-ray imaging of incremental tooth cementum shows two Early Jurass...

The fossil record of middle and late Miocene Eurasian hominoids has expanded considerably over the past few decades, particularly with the recovery of numerous isolated teeth and jaws. Scholars have turned to assessments of internal tooth structure and growth to make sense of the evolutionary radiations of these primates as well as their affinities...

An ancient Egyptian crocodile mummy (MHNL 90001591, Musée des Confluences, Lyon, France) dating to the Roman period and discovered at Kom -Ombo (Upper Egypt) was analysed through synchrotron multiscale microtomography. Using this advanced technology, the virtual autopsy of the animal was carried out without affecting the animal, balms and linen ban...

The growing availability of virtual cranial endocasts of extinct and extant vertebrates has fueled the quest for endocranial characters that discriminate between phylogenetic groups and resolve their neural significances. We used geometric morphometrics to compare a phylogenetically and ecologically comprehensive data set of archosaurian endocasts...

The neurocranium of sarcopterygian fishes was originally divided into an anterior (ethmosphenoid) and posterior (otoccipital) portion by an intracranial joint, and underwent major changes in its overall geometry before fusing into a single unit in lungfishes and early tetrapods¹. Although the pattern of these changes is well-documented, the develop...

The growth of long bones occurs in narrow discs of cartilage, called growth plates that provide a continuous supply of chondrocytes subsequently replaced by newly formed bone tissue. These growth plates are sandwiched between the bone shaft and a more distal bone structure called the secondary ossification center (SOC). We have recently shown that...

Several human dental traits typical of modern humans appear to be associated with the prolonged period of development that is a key human attribute. Understanding when, and in which early hominins, these dental traits first appeared is thus of strong interest. Using x-ray multiresolution synchrotron phase-contrast microtomography, we quantify denta...

Hyneria lindae is one of the largest Devonian sarcopterygians. It was found in the Catskill Formation (late Famennian) of Pennsylvania, USA. The current study focuses on the palaeohistology of the humerus of this tristichopterid and supports a low ossification rate and a late ossification onset in the appendicular skeleton. In addition to anatomica...

Scholars have debated the taxonomic identity of isolated primate teeth from the Asian Pleistocene for over a century, which is complicated by morphological and metric convergence between orangutan (Pongo) and hominin (Homo) molariform teeth. Like Homo erectus, Pongo once showed considerable dental variation and a wide distribution throughout mainla...

Seasonal variation in rainfall and temperature are major determinants of ecosystem structure and productivity and influence physical processes such as erosion rates and glaciation. By extension, seasonality can drive evolutionary change, and is hypothesized to have influenced early human subsistence and technological development. Rainfall patterns...

Archaeopteryx is an iconic fossil taxon with feathered wings from the Late Jurassic of Germany that occupies a crucial position for understanding the early evolution of avian flight. After over 150 years of study, its mosaic anatomy unifying characters of both non-flying dinosaurs and flying birds has remained challenging to interpret in a locomoto...