Eikonal phase retrieval: Unleashing the fourth generation sources potential for enhanced propagation based tomography on biological samples

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 would otherwise remain hidden under an excessive noise-to-signal ratio. Until today this possibility was hindered, in most objects of scientific interest, by the simultaneous presence of strong phase gradient regions and low contrast features. The strong gradients, when enhanced with the now possible long propagation distances, induce such strong phase effects that the linearisation assumptions of current state-of-the-art single-distance phase retrieval filters are broken, and the resulting image quality is jeopardized. Our work provides an innovative algorithm which efficiently performs the phase retrieval task over the entire near-field range, producing images of exceptional quality for mixed objects

New infant cranium from the African Miocene sheds light on ape evolution

The evolutionary history of extant hominoids (humans and apes) remains poorly understood. The African fossil record during the crucial time period, the Miocene epoch, largely comprises isolated jaws and teeth, and little is known about ape cranial evolution. Here we report on the, to our knowledge, most complete fossil ape cranium yet described, recovered from the 13 million-year-old Middle Miocene site of Napudet, Kenya. The infant specimen, KNM-NP 59050, is assigned to a new species of Nyanzapithecus on the basis of its unerupted permanent teeth, visualized by synchrotron imaging. Its ear canal has a fully ossified tubular ectotympanic, a derived feature linking the species with crown catarrhines. Although it resembles some hylobatids in aspects of its morphology and dental development, it possesses no definitive hylobatid synapomorphies. The combined evidence suggests that nyanzapithecines were stem hominoids close to the origin of extant apes, and that hylobatid-like facial features evolved multiple times during catarrhine evolution

Utilisation de technologies 3D en Archéologie : étude et médiation autour d’une momie égyptienne d’ibis

Il y a quelques semaines se sont déroulées les Journées Européennes du Patrimoine. A cette occasion, le Musée de Grenoble a organisé un petit événement ludique intitulé « Mystère à l’égyptienne ». Il s’agissait d’un jeu de piste à travers tout le parcours muséographique sur le thème de l’Égypte antique, de Champollion et du Docteur Clot-Bey. Fig. 1: Visuel de "Mystère à l'Égyptienne" organisé le 15 septembre 2018 dans le cadre des Journées Européennes du patrimoine (conception graphique : L..

Contribution de l’imagerie à rayonnement X Synchrotron à l’étude de la momification animale en Egypte antique : étude archéozoologique de momies de crocodiles (époques ptolémaïque et romaine)

Les anciens égyptiens ont momifié des millions d’animaux. Seule une toute petite partie de ces momies animales est parvenue jusqu’à nous, conservée dans divers musées. Les premières analyses pratiquées sur ces artéfacts ont conduit pour la plupart à leur destruction ou ont altéré leur état. Aujourd’hui il apparaît primordial de protéger ces précieux objets archéologiques. Des techniques non destructives et non invasives sont dorénavant utilisées, comme la Microtomographie à rayonnement X Synchrotron en contraste de phase de propagation (PPC-SRµCT). Cette technique a été appliquée à un corpus de 55 momies animales (49 crocodiles, cinq oiseaux, un chien) venant de trois musées distincts. L’application des méthodes archéozoologiques aux images virtuelles de la microtomographie a permis, d’une part, de formuler de nouvelles hypothèses concernant les modalités de gestion et de préparation des momies de crocodiles, et d’autre part, de proposer une interprétation de cette production en adéquation avec le calendrier de l’Égypte antique.The ancient Egyptians mummified millions of animals. Few of these animal mummies have made it to our museums. The first analyses carried out on these artefacts led most of them to destruction or to a very poor conservation. Today, it seems essential to protect these precious archaeological objects. Non-destructive and non-invasive techniques are now used, such as Propagation Phase Contrast Synchrotron X-ray Microtomography (PPC-SRµCT). This technique was applied to a corpus of 55 animal mummies (49 crocodiles, five birds, one dog) from three different museums. The application of archaeozoological methods to the virtual microtomography images allowed the formulation of new hypotheses concerning, on the one hand, the management and preparation of crocodile mummies, and on the other hand, to propose an interpretation of this production within the ancient Egyptian calendar

Nouvel éclairage sur une momie de crocodile au Synchrotron de Grenoble

Entre le Nouvel Empire et la période romaine, les Égyptiens ont momifié des millions d’animaux. La majeure partie de ces momies sont, ce que l’on pourrait appeler : des « momies votives ». Elles ont été produites en très grandes quantités, ce qui pose la question de l’approvisionnement en animaux nécessaires à cette « industrie ». Les égyptologues ont proposé plusieurs hypothèses : d’après des sources textuelles et archéologiques, les corps d’animaux déjà morts seraient utilisés pour la p..

Synchrotron virtual archaeozoology reveals how Ancient Egyptians prepared a decaying crocodile cadaver for mummification

International audienceAlthough 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 Musee des Confluences (Lyon, France). This state-of-the-art non-destructive imaging technique revealed the complete interior anatomy of the mummy in three dimensions. Here, we present detailed insight into the complex postmortem treatment of a decaying crocodile cadaver in preparation for mummification. Except for the head and the extremities of the limbs, everything beneath the skin of the crocodile (i.e. organs, muscles, and even most of the skeleton) was removed to cease further putrefaction. This unexpected finding demonstrates that earlier knowledge obtained from textual and other archaeological sources does not sufficiently reflect the diversity of mummification protocols implemented by Ancient Egyptians

Wild crocodiles hunted to make mummies in Roman Egypt: Evidence from synchrotron imaging

International audienc

New light shed on the early evolution of limb-bone growth plate and bone marrow

The production of blood cells (haematopoiesis) occurs in the limb bones of most tetrapods but is absent from 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 harsher environmental conditions. However little fossil evidence to support these hypotheses has been provided so far. Observations of the humeral microarchitecture of stem-tetrapods, batrachians and amniotes were performed using classical sectioning and three-dimensional synchrotron virtual histology. They show that Permian tetrapods seem to be among the first to exhibit a centralised marrow organisation which allows haematopoiesis as in extant amniotes. Not only does our study demonstrate that long-bone haematopoiesis was probably not an exaptation to the water-to-land transition but it sheds light on the early evolution of limb-bone development and the sequence of bone-marrow functional acquisitions

Automated segmentation of microtomography imaging of Egyptian mummies

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 the Automated SEgmentation of Microtomography Imaging (ASEMI) project, we developed a tool to automatically segment these volumetric images, using manually segmented samples to tune and train a machine learning model. For a set of four specimens of ancient Egyptian animal mummies we achieve an overall accuracy of 94–98% when compared with manually segmented slices, approaching the results of off-the-shelf commercial software using deep learning (97–99%) at much lower complexity. A qualitative analysis of the segmented output shows that our results are close in terms of usability to those from deep learning, justifying the use of these techniques.peer-reviewe