Bernadette S. de Bakker

An interactive three-dimensional digital atlas and quantitative database of human development

Digital reconstruction of human development The detailed morphology of human development has intrigued scientists and the medical field alike. However, the scarcity of specimens hampers detailed mapping of tissue architecture. Furthermore, inaccuracies in the description of human development have crept into textbooks from observations of animal models that are extrapolated to humans. By mapping normal developmental processes and patterns, such as the growth and relative placement of organs, congenital anomalies can be better understood. de Bakker et al. generated interactive three-dimensional digital reconstructions based on the Carnegie collection of histologically sectioned human embryos spanning the first 2 months of gestation. These interactive models will serve as educational and scientific resources for normal and abnormal human development. Science, this issue p. 10.1126/science.aag0053 Interactive three-dimensional models unveil early human development. INTRODUCTION The basic human body plan, the arrangement of organs in the body, is laid down during embryonic development. Insight into the formation of this plan informs researchers and clinicians about normal development versus the development of congenital malformations, the latter of which have an incidence of 3% in the human population and cause up to one-quarter of all neonatal deaths. Despite modern technologies such as three-dimensional imaging, the intricate morphogenesis of the developing human body is difficult to understand. Textbooks on human development are often based on the works of early embryologists, some published more than 100 years ago. Because of the limited availability of human embryonic specimens, it is difficult or impossible to independently verify the information carried in these textbooks, or even to assess whether this information is derived from studies on human or animal models. RATIONALE Current imaging and computer technology make it possible to reconstruct human development with sufficient resolution to visualize organ development. Stained histological sections (mainly from the Carnegie Collection of human embryos) were digitized, tissues and organs were identified, and knowledge-driven modeling was applied to correct imperfections in the three-dimensional reconstructions. RESULTS We created a digital atlas with 14 interactive three-dimensional models of human embryology and a database encompassing 34 embryos spanning the first 2 months of human development. Approximately 15,000 histological sections from the Carnegie Collection were analyzed by trained biomedical students under expert supervision, and up to 150 organs and structures were identified and digitally labeled in each section. The labeled structures were then spatially reconstructed in such a way that the relation between the reconstruction and the original images was preserved. We tested the reproducibility of the manual tracing of the different organs and found that the variability in volumes of segmented structures ranged from 0.3% to 2% between students for simple and complex structures, respectively. The 3D models, supplemented by an object tree with structures named in accordance with the international standard of embryonic terminology, the Terminologia Embryologica, are presented as interactive 3D-PDFs, which facilitates exploration of the complex relations between the different organs and allows researchers to develop an independent view of their spatial relations. The 3D reconstructions enable the measurement of the growth of the individual organs and structures, the assessment of the changing position of organs relative to vertebral segments during development, and the verification of remaining ambiguities in the descriptions of the development of organs. CONCLUSION The morphology presented in this atlas is directly connected to the original sections of the embryos in the Carnegie Collection—a connection that was in danger of being lost, with present-day textbook morphology becoming increasingly schematic and deviating from the original substrate. A number of detailed analyses of the development of the kidney, pharyngeal arch cartilages, and notochord show that the current descriptions of the development of these organs are based on comparative animal models rather than on factual observations in human specimens. These examples demonstrate the scientific value of the atlas. This atlas will therefore serve as an educational and reference resource for students, clinicians, and scientists interested in human development and development-related congenital diseases. The 3D-PDFs of the reconstructions, as well as original and labeled images, are freely available (http://3datlasofhumanembryology.com). Lateral views of a model of a 7.5-week-old human embryo (16 mm). Left: Skeletal system. Center: Cardiovascular system with transparent heart muscle. Venous system is shown in blue, arterial system in purple, liver vessels in red, and umbilical vein in pink. Right: Reconstructed organs, except skin. Note, for example, the neural tube in green and the nerves in yellow. Scale bar, 2.5 mm. Current knowledge about human development is based on the description of a limited number of embryonic specimens published in original articles and textbooks, often more than 100 years ago. It is exceedingly difficult to verify this knowledge, given the restricted availability of human embryos. We created a three-dimensional digital atlas and database spanning the first 2 months of human development, based on analysis of nearly 15,000 histological sections of the renowned Carnegie Collection of human embryonic specimens. We identified and labeled up to 150 organs and structures per specimen and made three-dimensional models to quantify growth, establish changes in the position of organs, and clarify current ambiguities. The atlas provides an educational and reference resource for studies on early human development, growth, and congenital malformations.

Towards a 3-dimensional atlas of the developing human embryo: The Amsterdam experience

Knowledge of complex morphogenetic processes that occur during embryonic development is essential for understanding anatomy and to get insight in the pathogenesis of congenital malformations. Understanding these processes can be facilitated by using a three-dimensional (3D) developmental series of human embryos, which we aim to create in this project. Digital images of serial sections of 34 human embryos of the Carnegie Collection between Carnegie stages 7 (15-17 days) and 23 (56-60 days) are used to create 3D reconstructions of different organ systems. The software package Amira is used to align the sections and to create the 3D reconstructions. In this midway evaluation we show the first results of the atlas, containing 34 embryos with more than 13.500 manually annotated sections. The 3D models can be interactively viewed within a 3D-pdf. This will be the first complete digital 3D human embryology atlas of this size, containing all developing organ systems.

The development of the human hyoid-larynx complex revisited: Hyoid-Larynx Complex Development Revisited

The hyoid–larynx complex is highly prone to anatomical variation. The etiology of anatomical variants such as Eagles syndrome and the aberrant hyoid apparatus can be explained from embryonic development. Modern textbooks state that the hyoid bone body develops from the second and third pharyngeal arch cartilages, and that thyroid cartilage derives from the fourth and sixth arch cartilages. This description, however, is incompatible with various anatomical variants, and it is unclear whether it was based on observations in human embryos or on comparative embryology.

The development of the human notochord

The notochord is a major regulator of embryonic patterning in vertebrates and abnormal notochordal development is associated with a variety of birth defects in man. Proper knowledge of the development of the human notochord, therefore, is important to understand the pathogenesis of these birth defects. Textbook descriptions vary significantly and seem to be derived from both human and animal data whereas the lack of references hampers verification of the presented data. Therefore, a verifiable and comprehensive description of the development of the human notochord is needed. Our analysis and three-dimensional (3D) reconstructions of 27 sectioned human embryos ranging from Carnegie Stage 8 to 15 (17–41 days of development), resulted in a comprehensive and verifiable new model of notochordal development. Subsequent to gastrulation, a transient group of cells briefly persists as the notochordal process which is incorporated into the endodermal roof of the gut while its dorsal side attaches to the developing neural tube. Then, the notochordal process embeds entirely into the endoderm, forming the epithelial notochordal plate, which remains intimately associated with the neural tube. Subsequently, the notochordal cells detach from the endoderm to form the definitive notochord, allowing the paired dorsal aortae to fuse between the notochord and the gut. We show that the formation of the notochordal process and plate proceeds in cranio-caudal direction. Moreover, in contrast to descriptions in the modern textbooks, we report that the formation of the definitive notochord in humans starts in the middle of the embryo, and proceeds in both cranial and caudal directions.

Hitherto unknown detailed muscle anatomy in an 8-week-old embryo

Congenital muscle diseases, such as myopathies or dystrophies, occur relatively frequently, with estimated incidences of up to 4.7 per 100 000 newborns. To diagnose congenital diseases in the early stages of pregnancy, and to interpret the results of increasingly advanced in utero imaging techniques, a profound knowledge of normal human morphological development of the locomotor system and the nervous system is necessary. Muscular development, however, is an often neglected topic or is only described in a general way in embryology textbooks and papers. To provide the required detailed and updated comprehensive picture of embryologic muscular anatomy, three‐dimensional (3D) reconstructions were created based on serial histological sections of a human embryo at Carnegie stage 23 (8 weeks of development, crown–rump length of 23.8 mm), using Amira reconstruction software. Reconstructed muscles, tendons, bones and nerves were exported in a 3D‐PDF file to permit interactive viewing. Almost all adult skeletal muscles of the trunk and limbs could be individually identified in their relative adult position. The pectoralis major muscle was divided in three separate muscle heads. The reconstructions showed remarkable highly developed extraocular, infrahyoid and suprahyoid muscles at this age but surprisingly also absence of the facial muscles that have been described to be present at this stage of development. The overall stage of muscle development suggests heterochrony of skeletal muscle development. Several individual muscle groups were found to be developed earlier and in more detail than described in current literature.

The value of post-mortem computed tomography of burned victims in a forensic setting

ObjectivesFire deaths are challenging fatalities for forensic pathologists, as the main question of whether death was due to the fire or not needs to be answered. In this retrospective study, we assessed whether post-mortem computed tomography (PMCT) has an added value prior to a forensic autopsy of burned victims.MethodsFrom 2008 to 2016, a PMCT was performed in 50 burned corpses prior to a complete forensic autopsy. In retrospect, all 50 PMCT scans were systematically assessed by a forensically experienced radiologist, masked from the autopsy reports. Subsequently, the PMCT findings were compared with the autopsy reports.ResultsHeat fractures, contractions and destruction of extremities, subcutaneous emphysema and post-mortem gas collections were easier to detect by PMCT compared to autopsy. Alterations by penetrating and blunt trauma and the presence of foreign bodies were easy to detect by PMCT as well by autopsy. PMCT was, however, not successful in detecting signs of vitality during the fire, detection of superficial thermal injuries and to answer the main question of the forensic autopsy, which is to investigate the cause of death.ConclusionsPMCT prior to autopsy is a valuable add-on in the post-mortem forensic investigation of burned victims for detection of hidden signs of trauma, gas collections and foreign bodies. However, since PMCT cannot answer the two main questions in forensic examination—determining the cause of death and detecting signs of vitality during the fire—it cannot replace an autopsy.Key Points• Post-mortem CT (PMCT) in burned victims shows hidden signs of trauma.• Foreign bodies and gas collections can easily be detected.• Cause of death and vitality signs cannot be assessed by PMCT.

Single-site neural tube closure in human embryos revisited

Since the multi‐site closure theory was first proposed in 1991 as explanation for the preferential localizations of neural tube defects, the closure of the neural tube has been debated. Although the multi‐site closure theory is much cited in clinical literature, single‐site closure is most apparent in literature concerning embryology. Inspired by Victor Hamburgers (1900–2001) statement that “our real teacher has been and still is the embryo, who is, incidentally, the only teacher who is always right”, we decided to critically review both theories of neural tube closure. To verify the theories of closure, we studied serial histological sections of 10 mouse embryos between 8.5 and 9.5 days of gestation and 18 human embryos of the Carnegie collection between Carnegie stage 9 (19–21 days) and 13 (28–32 days). Neural tube closure was histologically defined by the neuroepithelial remodeling of the two adjoining neural fold tips in the midline. We did not observe multiple fusion sites in neither mouse nor human embryos. A meta‐analysis of case reports on neural tube defects showed that defects can occur at any level of the neural axis. Our data indicate that the human neural tube fuses at a single site and, therefore, we propose to reinstate the single‐site closure theory for neural tube closure. We showed that neural tube defects are not restricted to a specific location, thereby refuting the reasoning underlying the multi‐site closure theory. Clin. Anat. 30:988–999, 2017.

The vanishing duodenal polyp: mesenteric invagination presenting as duodenal pseudopolyp

Duodenal polypoid masses are an uncommon finding mainly diagnosed incidentally at endoscopy or surgery. We report a 39-year-old female patient with symptoms of intermittent stabbing pain in the upper right abdominal quadrant and an iron deficiency anaemia, without complaints of weight loss, haematemesis or melaena. A duodenal polyp and acute duodenitis have been described during endoscopic examinations and CT and ultrasound. Surgical excision of the polyp was advised. Intraoperatively, an elongated duodenum was remarkable; however, at duodenotomy, no polyp was found, nor during intraoperative endoscopy. Looking back at the endoscopy and imaging results, it was noted that the polyp varied in size and location. It was therefore concluded that we dealt with the pseudopolyp phenomenon, caused by invagination of the duodenal wall and its mesentery into the duodenum, presenting as a lipomatous pseudopolyp. Telescopic invagination of the duodenal wall was facilitated by the elongated hypermobile duodenum.

Possible morphological substrates in the pathogenesis of arthritis

Acknowledgements: The authors thank Mrs. Jeanine Santermans, BioMed Research Centre, University of Hasselt, for her invaluable technical support during this study. Andrej Bezmaternykh and Youssef El Jerrari, BSc Students of Biomedical Sciences at the University of Hasselt, and Yasmina Azdud, Sebastiaan Deckers, Emiel Ectors, Erwin Leysen and Shamaila Naeem, MSc Students of Biomedical Sciences at the University of Hasselt, are thanked for their keen interest during the project.