The interactive presentation of 3D information obtained from reconstructed datasets and 3D placement of single histological sections with the 3D portable document format

Protocols for Generating Surfaces and Measuring 3D Organelle Morphology Using Amira

High-resolution 3D images of organelles are of paramount importance in cellular biology. Although light microscopy and transmission electron microscopy (TEM) have provided the standard for imaging cellular structures, they cannot provide 3D images. However, recent technological advances such as serial block-face scanning electron microscopy (SBF-SEM) and focused ion beam scanning electron microscopy (FIB-SEM) provide the tools to create 3D images for the ultrastructural analysis of organelles. Here, we describe a standardized protocol using the visualization software, Amira, to quantify organelle morphologies in 3D, thereby providing accurate and reproducible measurements of these cellular substructures. We demonstrate applications of SBF-SEM and Amira to quantify mitochondria and endoplasmic reticulum (ER) structures.

The osteology of the golden grey mullet Liza aurata (Teleostei: Mugiliformes: Mugilidae) including interactive three-dimensional reconstructions

Grey mullets are remarkably characterized by their overall uniform external morphology. Identifying species as well as positioning the Mugiliformes in a phylogenetic context is rather difficult. Most recently they were placed in the newly erected Ovalentaria, but more detailed relationships to potential sister taxa were not resolved. Studying the internal morphology, especially the osteology, might provide new insights into the evolution of the Mugiliformes as well as help clarify their phylogenetic position within the Ovalentaria. A detailed osteology of the golden grey mullet Liza aurata is presented. The use of cleared and stained specimens allowed for a complete examination of bony and cartilaginous structures, and a 3D reconstruction from a μCT data set provided additional information on the positional relationships of the bones. Following this, the data obtained were compared with different mugilid species, particularly with the flathead grey mullet Mugil cephalus. Several differences between these species could be identified, such as the position of the basisphenoid, the shape of the hyomandibular and the composition of the branchial arches. These characters might help in understanding the evolutionary changes happening within the mugiliforms and will provide the basis to study this taxon in detail, finally allowing the reconstruction of the body plan of grey mullets.

An interactive and intuitive visualisation method for X-ray computed tomography data of biological samples in 3D Portable Document Format

3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usually in the range of gigabytes and require specific and expensive software for rendering and interpretation. Here, we provide an advanced method for visualisation and interpretation of microCT data with small file formats, readable on all operating systems, using freely available Portable Document Format (PDF) software. Our method is based on the conversion of volumetric data into interactive 3D PDF, allowing rotation, movement, magnification and setting modifications of objects, thus providing an intuitive approach to analyse structures in a 3D context. We describe the complete pipeline from data acquisition, data processing and compression, to 3D PDF formatting on an example of craniofacial anatomical morphology in the mouse embryo. Our procedure is widely applicable in biological research and can be used as a framework to analyse volumetric data from any research field relying on 3D rendering and CT-biomedical imaging.

Communicating 3D data-interactive 3D PDF documents for expert reports and scientific publications in the field of forensic medicine

INTRODUCTION

Modern forensic investigations increasingly revert to 3D imaging techniques, such as computed tomography, magnetic resonance imaging, and 3D surface imaging. Findings are therefore often based on 3D data sets; however, this information is commonly reported and communicated within 2D imagery. The use of interactive 3D PDFs is already established in the scientific community but has yet to be implemented in the field of forensic medicine.

METHODS AND MATERIALS

Three example cases were chosen to serve as exemplary data for the most commonly applied imaging techniques in postmortem imaging. 3D surface models were created from postmortem magnetic resonance imaging (PMMR), postmortem computed tomography (PMCT), and 3D surface imaging data sets.

RESULTS

PMMR revealed a space-occupying subdural hemorrhage that led to ipsilateral compression of the brain tissue of the right hemisphere. PMCT displayed a defect in the skull on the left side of the temporal bone. 3D surface imaging data displayed a patterned discoloration on the inside of the left forearm.

DISCUSSION

Interactive 3D PDFs offer the possibility to communicate 3D information to the reader while maintaining all the benefits of a regular 2D PDF. With Adobe Acrobat, the reader can interactively navigate through 3D data sets and create sufficient depth cues to generate a realistic 3D perception of the data.

CONCLUSION

The interactive 3D PDF is a useful extension of standard 2D PDFs and has the potential to communicate 3D data to the reader in a more complete, more comprehensible, and less subjective manner than 2D PDFs.

Considerations for Measurement of Embryonic Organ Growth

Organogenesis is a complex coordinated process of cell proliferation, growth, migration, and apoptosis. Differential growth rates, particularly during cardiogenesis, play a role in establishing morphology. Studies using stereological and cell sorting methods derive averages of morphogenetic parameters for an organ. To understand tissue composition and differential growth, the researcher must determine a number of morphogenetic parameters in the developing organ. Such measurements require sectioning to enable identification of organ borders, tissue components and cell types, three-dimensional (3D)-reconstruction of sections to visualize morphology and a 3D-measurement scheme to build local morphogenetic information. Although thick the section confocal microscopy partially solves these issues, information loss at the section surface hampers the reconstruction of 3D morphology. Episcopic imaging provides the correct morphology but lacks histological procedures to identify multiple cell types. The 3D-measurement scheme is based on systematic sampling, with overlapping sample volumes, of the entire organ in the aligned image stack. For each sample volume, morphogenetic variables are calculated and results projected back to the cube (boxel) at the sample volume center. Boxel size determines spatial resolution of the final quantitative 3D-reconstruction whereas size of the sample volume determines the precision of the morphogenetic information. The methods described here can be used to measure tissue volume, proliferation and cell size, to determine contribution and distribution of cell types in a tissue and to display this information in a quantitative 3D-reconstruction. Anat Rec, 302:49-57, 2019. © 2018 Wiley Periodicals, Inc.

Three-Dimensional Portable Document Format (3D PDF) in Clinical Communication and Biomedical Sciences: Systematic Review of Applications, Tools, and Protocols

Background

The Portable Document Format (PDF) is the standard file format for the communication of biomedical information via the internet and for electronic scholarly publishing. Although PDF allows for the embedding of three-dimensional (3D) objects and although this technology has great potential for the communication of such data, it is not broadly used by the scientific community or by clinicians.

Objective

The objective of this review was to provide an overview of existing publications that apply 3D PDF technology and the protocols and tools for the creation of model files and 3D PDFs for scholarly purposes to demonstrate the possibilities and the ways to use this technology.

Methods

A systematic literature review was performed using PubMed and Google Scholar. Articles searched for were in English, peer-reviewed with biomedical reference, published since 2005 in a journal or presented at a conference or scientific meeting. Ineligible articles were removed after screening. The found literature was categorized into articles that (1) applied 3D PDF for visualization, (2) showed ways to use 3D PDF, and (3) provided tools or protocols for the creation of 3D PDFs or necessary models. Finally, the latter category was analyzed in detail to provide an overview of the state of the art.

Results

The search retrieved a total of 902 items. Screening identified 200 in-scope publications, 13 covering the use of 3D PDF for medical purposes. Only one article described a clinical routine use case; all others were pure research articles. The disciplines that were covered beside medicine were many. In most cases, either animal or human anatomies were visualized. A method, protocol, software, library, or other tool for the creation of 3D PDFs or model files was described in 19 articles. Most of these tools required advanced programming skills and/or the installation of further software packages. Only one software application presented an all-in-one solution with a graphical user interface.

Conclusions

The use of 3D PDF for visualization purposes in clinical communication and in biomedical publications is still not in common use, although both the necessary technique and suitable tools are available, and there are many arguments in favor of this technique. The potential of 3D PDF usage should be disseminated in the clinical and biomedical community. Furthermore, easy-to-use, standalone, and free-of-charge software tools for the creation of 3D PDFs should be developed.

Control of cardiac jelly dynamics by NOTCH1 and NRG1 defines the building plan for trabeculation

In vertebrate hearts, the ventricular trabecular myocardium develops as a sponge-like network of cardiomyocytes that is critical for contraction and conduction, ventricular septation, papillary muscle formation and wall thickening through the process of compaction ¹ . Defective trabeculation leads to embryonic lethality^2-4 or non-compaction cardiomyopathy (NCC) ⁵ . There are divergent views on when and how trabeculation is initiated in different species. In zebrafish, trabecular cardiomyocytes extrude from compact myocardium ⁶ , whereas in chicks, chamber wall thickening occurs before overt trabeculation ⁷ . In mice, the onset of trabeculation has not been described, but is proposed to begin at embryonic day 9.0, when cardiomyocytes form radially oriented ribs ² . Endocardium-myocardium communication is essential for trabeculation, and numerous signalling pathways have been identified, including Notch^2,8 and Neuregulin (NRG) ⁴ . Late disruption of the Notch pathway causes NCC ⁵ . Whereas it has been shown that mutations in the extracellular matrix (ECM) genes Has2 and Vcan prevent the formation of trabeculae in mice^9,10 and the matrix metalloprotease ADAMTS1 promotes trabecular termination ³ , the pathways involved in ECM dynamics and the molecular regulation of trabeculation during its early phases remain unexplored. Here we present a model of trabeculation in mice that integrates dynamic endocardial and myocardial cell behaviours and ECM remodelling, and reveal new epistatic relationships between the involved signalling pathways. NOTCH1 signalling promotes ECM degradation during the formation of endocardial projections that are critical for individualization of trabecular units, whereas NRG1 promotes myocardial ECM synthesis, which is necessary for trabecular rearrangement and growth. These systems interconnect through NRG1 control of Vegfa, but act antagonistically to establish trabecular architecture. These insights enabled the prediction of persistent ECM and cardiomyocyte growth in a mouse NCC model, providing new insights into the pathophysiology of congenital heart disease.

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 development of the human hyoid-larynx complex revisited

OBJECTIVES/HYPOTHESIS

The hyoid-larynx complex is highly prone to anatomical variation. The etiology of anatomical variants such as Eagle's 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.

STUDY DESIGN

14 human embryos from the Carnegie collection between Carnegie stage 17 and 23 (42-60 days) were selected based on their histological quality.

METHODS

Histological sections of the selected embryos were examined. Three-dimensional models were prepared in an interactive format. These anatomical models provide crucial spatial information and facilitate interpretation.

RESULTS

We observed a less-complicated development of the hyoid-larynx complex than is currently described in textbooks. The body of the hyoid bone originates from a single growth center, without overt contributions from second and third pharyngeal arch cartilages. The fourth and sixth arch cartilages were not detected in human embryos; the thyroid and cricoid cartilages develop as mesenchymal condensations in the neck region.

CONCLUSIONS

Despite new research techniques, theories about hyoid-larynx complex development from the beginning of the 20th century have not been refuted properly and can still be found in modern literature. Based on observations in human embryos, we propose a new and relatively simple description of the development of the hyoid-larynx complex to facilitate better understanding of the etiology of anatomical variants.

LEVEL OF EVIDENCE

NA Laryngoscope, 1829-1834, 2018.

Architectural differences in the anterior and middle compartments of the pelvic floor of young-adult and postmenopausal females

The pelvic floor guards the passage of the pelvic organs to the exterior. The near-epidemic prevalence of incontinence in women continues to generate interest in the functional anatomy of the pelvic floor. However, due to its complex architecture and poor accessibility, the classical 'dissectional' approach has been unable to come up with a satisfactory description, so that many aspects of its anatomy continue to raise debate. For this reason, we opted for a 'sectional' approach, using the Chinese Visible Human project (four females, 21-35 years) and the Visible Human Project (USA; one female, 59 years) datasets to investigate age-related changes in the architecture of the anterior and middle compartments of the pelvic floor. The puborectal component of the levator ani muscle defined the levator hiatus boundary. The urethral sphincter complex consisted of a circular proximal portion (urethral sphincter proper), a sling that passed on the vaginal wall laterally to attach to the puborectal muscle (urethral compressor), and a circular portion that surrounded the distal urethra and vagina (urethrovaginal sphincter). The exclusive attachment of the urethral sphincter to soft tissues implies dependence on pelvic-floor integrity for optimal function. The vagina was circular at the introitus and gradually flattened between bladder and rectum. Well-developed fibrous tissue connected the inferior vaginal wall with urethra, rectum and pelvic floor. With eight-muscle insertions, the perineal body was a strong, irregular fibrous node that guarded the levator hiatus. Only loose areolar tissue comprising a remarkably well developed venous plexus connecting the middle and superior parts of the vagina with the lateral pelvic wall. The posterolateral boundary of the putative cardinal and sacrouterine ligaments coincided with the adventitia surrounding the mesorectum. The major difference between the young-adult and postmenopausal pelvic floor was the expansion of fat in between the components of the pelvic floor. We hypothesize that accumulation of pelvic fat compromises pelvic-floor cohesion, because the pre-pubertal pelvis contains very little fibrous and adipose tissue, and fat is an excellent lubricant.

Sequential Notch activation regulates ventricular chamber development

Ventricular chambers are essential for the rhythmic contraction and relaxation occurring in every heartbeat throughout life. Congenital abnormalities in ventricular chamber formation cause severe human heart defects. How the early trabecular meshwork of myocardial fibres forms and subsequently develops into mature chambers is poorly understood. We show that Notch signalling first connects chamber endocardium and myocardium to sustain trabeculation, and later coordinates ventricular patterning and compaction with coronary vessel development to generate the mature chamber, through a temporal sequence of ligand signalling determined by the glycosyltransferase manic fringe (MFng). Early endocardial expression of MFng promotes Dll4-Notch1 signalling, which induces trabeculation in the developing ventricle. Ventricular maturation and compaction require MFng and Dll4 downregulation in the endocardium, which allows myocardial Jag1 and Jag2 signalling to Notch1 in this tissue. Perturbation of this signalling equilibrium severely disrupts heart chamber formation. Our results open a new research avenue into the pathogenesis of cardiomyopathies.

Regional differences in WT-1 and Tcf21 expression during ventricular development: implications for myocardial compaction

BACKGROUND

Morphological and functional differences of the right and left ventricle are apparent in the adult human heart. A differential contribution of cardiac fibroblasts and smooth muscle cells (populations of epicardium-derived cells) to each ventricle may account for part of the morphological-functional disparity. Here we studied the relation between epicardial derivatives and the development of compact ventricular myocardium.

RESULTS

Wildtype and Wt1CreERT2/+ reporter mice were used to study WT-1 expressing cells, and Tcf21lacZ/+ reporter mice and PDGFRα-/-;Tcf21LacZ/+ mice to study the formation of the cardiac fibroblast population. After covering the heart, intramyocardial WT-1+ cells were first observed at the inner curvature, the right ventricular postero-lateral wall and left ventricular apical wall. Later, WT-1+ cells were present in the walls of both ventricles, but significantly more pronounced in the left ventricle. Tcf21-LacZ + cells followed the same distribution pattern as WT-1+ cells but at later stages, indicating a timing difference between these cell populations. Within the right ventricle, WT-1+ and Tcf21-lacZ+ cell distribution was more pronounced in the posterior inlet part. A gradual increase in myocardial wall thickness was observed early in the left ventricle and at later stages in the right ventricle. PDGFRα-/-;Tcf21LacZ/+ mice showed deficient epicardium, diminished number of Tcf21-LacZ + cells and reduced ventricular compaction.

CONCLUSIONS

During normal heart development, spatio-temporal differences in contribution of WT-1 and Tcf21-LacZ + cells to right versus left ventricular myocardium occur parallel to myocardial thickening. These findings may relate to lateralized differences in ventricular (patho)morphology in humans.

3D Topography of the Young Adult Anal Sphincter Complex Reconstructed from Undeformed Serial Anatomical Sections

Background

Pelvic-floor anatomy is usually studied by artifact-prone dissection or imaging, which requires prior anatomical knowledge. We used the serial-section approach to settle contentious issues and an interactive 3D-pdf to make the results widely accessible.

Method

3D reconstructions of undeformed thin serial anatomical sections of 4 females and 2 males (21–35y) of the Chinese Visible Human database.

Findings

Based on tendinous septa and muscle-fiber orientation as segmentation guides, the anal-sphincter complex (ASC) comprised the subcutaneous external anal sphincter (EAS) and the U-shaped puborectal muscle, a part of the levator ani muscle (LAM). The anococcygeal ligament fixed the EAS to the coccygeal bone. The puborectal-muscle loops, which define the levator hiatus, passed around the anorectal junction and inserted anteriorly on the perineal body and pubic bone. The LAM had a common anterior attachment to the pubic bone, but separated posteriorly into puborectal and “pubovisceral” muscles. This pubovisceral muscle was bilayered: its internal layer attached to the conjoint longitudinal muscle of the rectum and the rectococcygeal fascia, while its outer, patchy layer reinforced the inner layer. ASC contraction makes the ano-rectal bend more acute and lifts the pelvic floor. Extensions of the rectal longitudinal smooth muscle to the coccygeal bone (rectococcygeal muscle), perineal body (rectoperineal muscle), and endopelvic fascia (conjoint longitudinal and pubovisceral muscles) formed a “diaphragm” at the inferior boundary of the mesorectum that suspended the anorectal junction. Its contraction should straighten the anorectal bend.

Conclusion

The serial-section approach settled contentious topographic issues of the pelvic floor. We propose that the ASC is involved in continence and the rectal diaphragm in defecation.

The growth pattern of the human intestine and its mesentery

BACKGROUND

It remains unclear to what extent midgut rotation determines human intestinal topography and pathology. We reinvestigated the midgut during its looping and herniation phases of development, using novel 3D visualization techniques.

RESULTS

We distinguished 3 generations of midgut loops. The topography of primary and secondary loops was constant, but that of tertiary loops not. The orientation of the primary loop changed from sagittal to transverse due to the descent of ventral structures in a body with a still helical body axis. The 1st secondary loop (duodenum, proximal jejunum) developed intraabdominally towards a left-sided position. The 2nd secondary loop (distal jejunum) assumed a left-sided position inside the hernia before returning, while the 3rd and 4th secondary loops retained near-midline positions. Intestinal return into the abdomen resembled a backward sliding movement. Only after return, the 4th secondary loop (distal ileum, cecum) rapidly "slid" into the right lower abdomen. The seemingly random position of the tertiary small-intestinal loops may have a biomechanical origin.

CONCLUSIONS

The interpretation of "intestinal rotation" as a mechanistic rather than a descriptive concept underlies much of the confusion accompanying the physiological herniation. We argue, instead, that the concept of "en-bloc rotation" of the developing midgut is a fallacy of schematic drawings. Primary, secondary and tertiary loops arise in a hierarchical fashion. The predictable position and growth of secondary loops is pre-patterned and determines adult intestinal topography. We hypothesize based on published accounts that malrotations result from stunted development of secondary loops.

The sinus venosus myocardium contributes to the atrioventricular canal: potential role during atrioventricular node development?

The presence of distinct electrophysiological pathways within the atrioventricular node (AVN) is a prerequisite for atrioventricular nodal reentrant tachycardia to occur. In this study, the different cell contributions that may account for the anatomical and functional heterogeneity of the AVN were investigated. To study the temporal development of the AVN, the expression pattern of ISL1, expressed in cardiac progenitor cells, was studied in sequential stages performing co-staining with myocardial markers (TNNI2 and NKX2-5) and HCN4 (cardiac conduction system marker). An ISL1+/TNNI2+/HCN4+ continuity between the myocardium of the sinus venosus and atrioventricular canal was identified in the region of the putative AVN, which showed a pacemaker-like phenotype based on single cell patch-clamp experiments. Furthermore, qPCR analysis showed that even during early development, different cell populations can be identified in the region of the putative AVN. Fate mapping was performed by in ovo vital dye microinjection. Embryos were harvested and analysed 24 and 48 hrs post-injection. These experiments showed incorporation of sinus venosus myocardium in the posterior region of the atrioventricular canal. The myocardium of the sinus venosus contributes to the atrioventricular canal. It is postulated that the myocardium of the sinus venosus contributes to nodal extensions or transitional cells of the AVN since these cells are located in the posterior region of the AVN. This finding may help to understand the origin of atrioventricular nodal reentrant tachycardia.

Application and evaluation of interactive 3D PDF for presenting and sharing planning results for liver surgery in clinical routine

Background & Objectives

The Portable Document Format (PDF) is the de-facto standard for the exchange of electronic documents. It is platform-independent, suitable for the exchange of medical data, and allows for the embedding of three-dimensional (3D) surface mesh models. In this article, we present the first clinical routine application of interactive 3D surface mesh models which have been integrated into PDF files for the presentation and the exchange of Computer Assisted Surgery Planning (CASP) results in liver surgery. We aimed to prove the feasibility of applying 3D PDF in medical reporting and investigated the user experience with this new technology.

Methods

We developed an interactive 3D PDF report document format and implemented a software tool to create these reports automatically. After more than 1000 liver CASP cases that have been reported in clinical routine using our 3D PDF report, an international user survey was carried out online to evaluate the user experience.

Results

Our solution enables the user to interactively explore the anatomical configuration and to have different analyses and various resection proposals displayed within a 3D PDF document covering only a single page that acts more like a software application than like a typical PDF file (“PDF App”). The new 3D PDF report offers many advantages over the previous solutions. According to the results of the online survey, the users have assessed the pragmatic quality (functionality, usability, perspicuity, efficiency) as well as the hedonic quality (attractiveness, novelty) very positively.

Conclusion

The usage of 3D PDF for reporting and sharing CASP results is feasible and well accepted by the target audience. Using interactive PDF with embedded 3D models is an enabler for presenting and exchanging complex medical information in an easy and platform-independent way. Medical staff as well as patients can benefit from the possibilities provided by 3D PDF. Our results open the door for a wider use of this new technology, since the basic idea can and should be applied for many medical disciplines and use cases.

Extreme variation in the atrial septation of caecilians (Amphibia: Gymnophiona)

Caecilians (order Gymnophiona) are elongate, limbless, snake-like amphibians that are the sister-group (closest relatives) of all other recent amphibians (frogs and salamanders). Little is known of their cardiovascular anatomy and physiology, but one nearly century old study suggests that Hypogeophis (family Indotyphlidae), commonly relied upon as a representative caecilian species, has atrial septation in the frontal plane and more than one septum. In contrast, in other vertebrates there generally is one atrial septum in the sagittal plane. We studied the adult heart of Idiocranium (also Indotyphlidae) using immunohistochemistry and confirm that the interatrial septum is close to the frontal plane. Additionally, a parallel right atrial septum divides three-fourths of the right atrial cavity of this species. Idiocranium embryos in the Hill collection reveal that atrial septation initiates in the sagittal plane as in other tetrapods. Late developmental stages, however, see a left-ward shift of visceral organs and a concordant rotation of the atria that reorients the atrial septa towards the frontal plane. The gross anatomies of species from six other caecilian families reveal that (i) the right atrial septum developed early in caecilian evolution (only absent in Rhinatrematidae) and that (ii) rotation of the atria evolved later and its degree varies between families. In most vertebrates a prominent atrial trabeculation associates with the sinuatrial valve, the so-called septum spurium, and the right atrial septum seems homologous to this trabeculation but much more developed. The right atrial septum does not appear to be a consequence of body elongation because it is absent in some caecilians and in snakes. The interatrial septum of caecilians shares multiple characters with the atrial septum of lungfishes, salamanders and the embryonic septum primum of amniotes. In conclusion, atrial septation in caecilians is based on evolutionarily conserved structures but possibly exhibits greater variation than in any other vertebrate order.

Simplified generation of biomedical 3D surface model data for embedding into 3D portable document format (PDF) files for publication and education

The usefulness of the 3D Portable Document Format (PDF) for clinical, educational, and research purposes has recently been shown. However, the lack of a simple tool for converting biomedical data into the model data in the necessary Universal 3D (U3D) file format is a drawback for the broad acceptance of this new technology. A new module for the image processing and rapid prototyping framework MeVisLab does not only provide a platform-independent possibility to create surface meshes out of biomedical/DICOM and other data and to export them into U3D – it also lets the user add meta data to these meshes to predefine colors and names that can be processed by a PDF authoring software while generating 3D PDF files. Furthermore, the source code of the respective module is available and well documented so that it can easily be modified for own purposes.

Development of the hearts of lizards and snakes and perspectives to cardiac evolution

Birds and mammals both developed high performance hearts from a heart that must have been reptile-like and the hearts of extant reptiles have an unmatched variability in design. Yet, studies on cardiac development in reptiles are largely old and further studies are much needed as reptiles are starting to become used in molecular studies. We studied the growth of cardiac compartments and changes in morphology principally in the model organism corn snake (Pantherophis guttatus), but also in the genotyped anole (Anolis carolinenis and A. sagrei) and the Philippine sailfin lizard (Hydrosaurus pustulatus). Structures and chambers of the formed heart were traced back in development and annotated in interactive 3D pdfs. In the corn snake, we found that the ventricle and atria grow exponentially, whereas the myocardial volumes of the atrioventricular canal and the muscular outflow tract are stable. Ventricular development occurs, as in other amniotes, by an early growth at the outer curvature and later, and in parallel, by incorporation of the muscular outflow tract. With the exception of the late completion of the atrial septum, the adult design of the squamate heart is essentially reached halfway through development. This design strongly resembles the developing hearts of human, mouse and chicken around the time of initial ventricular septation. Subsequent to this stage, and in contrast to the squamates, hearts of endothermic vertebrates completely septate their ventricles, develop an insulating atrioventricular plane, shift and expand their atrioventricular canal toward the right and incorporate the systemic and pulmonary venous myocardium into the atria.

Development of the human aortic arch system captured in an interactive three-dimensional reference model

Variations and mutations in the human genome, such as 22q11.2 microdeletion, can increase the risk for congenital defects, including aortic arch malformations. Animal models are increasingly expanding our molecular and genetic insights into aortic arch development. However, in order to justify animal-to-human extrapolations, a human morphological, and molecular reference model would be of great value, but is currently lacking. Here, we present interactive three-dimensional reconstructions of the developing human aortic arch system, supplemented with the protein distribution of developmental markers for patterning and growth, including T-box transcription factor TBX1, a major candidate for the phenotypes found in patients with the 22q11.2 microdeletion. These reconstructions and expression data facilitate unbiased interpretations, and reveal previously unappreciated aspects of human aortic arch development. Based on our reconstructions and on reported congenital anomalies of the pulmonary trunk and tributaries, we postulate that the pulmonary arteries originate from the aortic sac, rather than from the sixth pharyngeal arch arteries. Similar to mouse, TBX1 is expressed in pharyngeal mesenchyme and epithelia. The endothelium of the pharyngeal arch arteries is largely negative for TBX1 and family member TBX2 but expresses neural crest marker AP2α, which gradually decreases with ongoing development of vascular smooth muscle. At early stages, the pharyngeal arch arteries, aortic sac, and the dorsal aortae in particular were largely negative for proliferation marker Ki67, potentially an important parameter during aortic arch system remodeling. Together, our data support current animal-to-human extrapolations and future genetic and molecular analyses using animal models of congenital heart disease. © 2013 Wiley Periodicals, Inc.

From 2D to 3D: Construction of a 3D Parametric Model for Detection of Dental Roots Shape and Position from a Panoramic Radiograph-A Preliminary Report

Objectives. To build a 3D parametric model to detect shape and volume of dental roots, from a panoramic radiograph (PAN) of the patient. Materials and Methods. A PAN and a cone beam computed tomography (CBCT) of a patient were acquired. For each tooth, various parameters were considered (coronal and root lengths and widths): these were measured from the CBCT and from the PAN. Measures were compared to evaluate the accuracy level of PAN measurements. By using a CAD software, parametric models of an incisor and of a molar were constructed employing B-spline curves and free-form surfaces. PAN measures of teeth 2.1 and 3.6 were assigned to the parametric models; the same two teeth were segmented from CBCT. The two models were superimposed to assess the accuracy of the parametric model. Results. PAN measures resulted to be accurate and comparable with all other measurements. From model superimposition the maximum error resulted was 1.1 mm on the incisor crown and 2 mm on the molar furcation. Conclusion. This study shows that it is possible to build a 3D parametric model starting from 2D information with a clinically valid accuracy level. This can ultimately lead to a crown-root movement simulation.

Measurement and 3D-visualization of cell-cycle length using double labelling with two thymidine analogues applied in early heart development

Organ development is a complex spatial process in which local differences in cell proliferation rate play a key role. Understanding this role requires the measurement of the length of the cell cycle at every position of the three-dimensional (3D) structure. This measurement can be accomplished by exposing the developing embryo to two different thymidine analogues for two different durations immediately followed by tissue fixation. This paper presents a method and a dedicated computer program to measure the resulting labelling indices and subsequently calculate and visualize local cell cycle lengths within the 3D morphological context of a developing organ. By applying this method to the developing heart, we show a large difference in cell cycle lengths between the early heart tube and the adjacent mesenchyme of the pericardial wall. Later in development, a local increase in cell size was found to be associated with a decrease in cell cycle length in the region where the chamber myocardium starts to develop. The combined application of halogenated-thymidine double exposure and image processing enables the automated study of local cell cycle parameters in single specimens in a full 3D context. It can be applied in a wide range of research fields ranging from embryonic development to tissue regeneration and cancer research.

Heart repair: from natural mechanisms of cardiomyocyte production to the design of new cardiac therapies

Most organs in mammals, including the heart, show a certain level of plasticity and repair ability during gestation. This plasticity is, however, compromised for many organs in adulthood, resulting in the inability to repair organ injury, including heart damage produced by acute or chronic ischemic conditions. In contrast, lower vertebrates, such as fish or amphibians, retain a striking regenerative ability during their entire life, being able to repair heart injuries. There is a great interest in understanding both the mechanisms that allow heart plasticity during mammalian fetal life and those that permit adult cardiac regeneration in zebrafish. Here, we revise strategies for cardiomyocyte production during development and in response to injury and discuss differential regeneration ability of teleosts and mammals. Understanding these mechanisms may allow establishing alternative therapeutic approaches to cope with heart failure in humans.

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.

Growth of the developing mouse heart: an interactive qualitative and quantitative 3D atlas

Analysis of experiments aimed at understanding the genetic mechanisms of differentiation and growth of the heart, calls for detailed insights into cardiac growth and proliferation rate of myocytes and their precursors. Such insights in mouse heart development are currently lacking. We quantitatively assessed the 3D patterns of proliferation in the forming mouse heart and in the adjacent splanchnic mesoderm, from the onset of heart formation till the developed heart at late gestation. These results are presented in an interactive portable document format (Suppl. PDF) to facilitate communication and understanding. We show that the mouse splanchnic mesoderm is highly proliferative, and that the proliferation rate drops upon recruitment of cells into the cardiac lineage. Concomitantly, the proliferation rate locally increases at the sites of chamber formation, generating a regionalized proliferation pattern. Quantitative analysis shows a gradual decrease in proliferation rate of the ventricular walls with progression of development, and a base-to-top decline in proliferation rate in the trabecules. Our data offers clear insights into the growth and morphogenesis of the mouse heart and shows that in early development the phases of tube formation and chamber formation overlap. The resulting interactive quantitative 3D atlas of cardiac growth and morphogenesis provides a resource for interpretation of mechanistic studies.

Biomedical informatics--a confluence of disciplines?

BACKGROUND

Biomedical informatics is a broad discipline that borrows many methods and techniques from other disciplines.

OBJECTIVE

To reflect a) on the character of biomedical informatics and to determine whether it is multi-disciplinary or inter-disciplinary; b) on the question whether biomedical informatics is more than the sum of its supporting disciplines and c) on the position of biomedical informatics with respect to related disciplines.

METHOD

Inviting an international group of experts in biomedical informatics and related disciplines on the occasion of the 50th anniversary of Methods of Information in Medicine to present their viewpoints.

RESULTS AND CONCLUSIONS

This paper contains the reflections of a number of the invited experts on the character of biomedical informatics. Most of the authors agree that biomedical informatics is an interdisciplinary field of study where researchers with different scientific backgrounds alone or in combination carry out research. Biomedical informatics is a very broad scientific field and still expanding, yet comprised of a constructive aspect (designing and building systems). One author expressed that the essence of biomedical informatics, as opposed to related disciplines, lies in the modelling of the biomedical content. Interdisciplinarity also has consequences for education. Maintaining rigid disciplinary structures does not allow for sufficient adaptability to capitalize on important trends nor to leverage the influences these trends may have on biomedical informatics. It is therefore important for students to become aware of research findings in related disciplines. In this respect, it was also noted that the fact that many scientific fields use different languages and that the research findings are stored in separate bibliographic databases makes it possible that potentially connected findings will never be linked, despite the fact that these findings were published. Bridges between the sciences are needed for the success of biomedical informatics.

Three-dimensional and molecular analysis of the arterial pole of the developing human heart

Labeling experiments in chicken and mouse embryos have revealed important roles for different cell lineages in the development of the cardiac arterial pole. These data can only fully be exploited when integrated into the continuously changing morphological context and compared with the patterns of gene expression. As yet, studies on the formation of separate ventricular outlets and arterial trunks in the human heart are exclusively based on histologically stained sections. So as to expand these studies, we performed immunohistochemical analyses of serially sectioned human embryos, along with three-dimensional reconstructions. The development of the cardiac arterial pole involves several parallel and independent processes of formation and fusion of outflow tract cushions, remodeling of the aortic sac and closure of an initial aortopulmonary foramen through formation of a transient aortopulmonary septum. Expression patterns of the transcription factors ISL1, SOX9 and AP2α show that, in addition to fusion of the SOX9-positive endocardial cushions, intrapericardial protrusion of pharyngeal mesenchyme derived from the neural crest contributes to the separation of the developing ascending aorta from the pulmonary trunk. The non-adjacent walls of the intrapericardial arterial trunks are formed through addition of ISL1-positive cells to the distal outflow tract, while the facing parts of the walls form from the protruding mesenchyme. The morphogenetic steps, along with the gene expression patterns reported in this study, are comparable to those observed in the mouse. They confirm the involvement of mesenchymal tissues derived from endocardium, mesoderm and migrating neural crest cells in the process of initial septation of the distal part of the outflow tract, and its subsequent separation into discrete intrapericardial arterial trunks.

Three-dimensional reconstructions of intrahepatic bile duct tubulogenesis in human liver

Background

During liver development, intrahepatic bile ducts are thought to arise by a unique asymmetric mode of cholangiocyte tubulogenesis characterized by a series of remodeling stages. Moreover, in liver diseases, cells lining the Canals of Hering can proliferate and generate new hepatic tissue. The aim of this study was to develop protocols for three-dimensional visualization of protein expression, hepatic portal structures and human hepatic cholangiocyte tubulogenesis.

Results

Protocols were developed to digitally visualize portal vessel branching and protein expression of hepatic cell lineage and extracellular matrix deposition markers in three dimensions. Samples from human prenatal livers ranging from 7 weeks + 2 days to 15½ weeks post conception as well as adult normal and acetaminophen intoxicated liver were used. The markers included cytokeratins (CK) 7 and 19, the epithelial cell adhesion molecule (EpCAM), hepatocyte paraffin 1 (HepPar1), sex determining region Y (SRY)-box 9 (SOX9), laminin, nestin, and aquaporin 1 (AQP1).

Digital three-dimensional reconstructions using CK19 as a single marker protein disclosed a fine network of CK19 positive cells in the biliary tree in normal liver and in the extensive ductular reactions originating from intrahepatic bile ducts and branching into the parenchyma of the acetaminophen intoxicated liver. In the developing human liver, three-dimensional reconstructions using multiple marker proteins confirmed that the human intrahepatic biliary tree forms through several developmental stages involving an initial transition of primitive hepatocytes into cholangiocytes shaping the ductal plate followed by a process of maturation and remodeling where the intrahepatic biliary tree develops through an asymmetrical form of cholangiocyte tubulogenesis.

Conclusions

The developed protocols provide a novel and sophisticated three-dimensional visualization of vessels and protein expression in human liver during development and disease.

The BMP antagonist follistatin-like 1 is required for skeletal and lung organogenesis

Follistatin-like 1 (Fstl1) is a secreted protein of the BMP inhibitor class. During development, expression of Fstl1 is already found in cleavage stage embryos and becomes gradually restricted to mesenchymal elements of most organs during subsequent development. Knock down experiments in chicken and zebrafish demonstrated a role as a BMP antagonist in early development. To investigate the role of Fstl1 during mouse development, a conditional Fstl1 KO allele as well as a Fstl1-GFP reporter mouse were created. KO mice die at birth from respiratory distress and show multiple defects in lung development. Also, skeletal development is affected. Endochondral bone development, limb patterning as well as patterning of the axial skeleton are perturbed in the absence of Fstl1. Taken together, these observations show that Fstl1 is a crucial regulator in BMP signalling during mouse development.

Development of the pulmonary vein and the systemic venous sinus: an interactive 3D overview

Knowledge of the normal formation of the heart is crucial for the understanding of cardiac pathologies and congenital malformations. The understanding of early cardiac development, however, is complicated because it is inseparably associated with other developmental processes such as embryonic folding, formation of the coelomic cavity, and vascular development. Because of this, it is necessary to integrate morphological and experimental analyses. Morphological insights, however, are limited by the difficulty in communication of complex 3D-processes. Most controversies, in consequence, result from differences in interpretation, rather than observation. An example of such a continuing debate is the development of the pulmonary vein and the systemic venous sinus, or “sinus venosus”. To facilitate understanding, we present a 3D study of the developing venous pole in the chicken embryo, showing our results in a novel interactive fashion, which permits the reader to form an independent opinion. We clarify how the pulmonary vein separates from a greater vascular plexus within the splanchnic mesoderm. The systemic venous sinus, in contrast, develops at the junction between the splanchnic and somatic mesoderm. We discuss our model with respect to normal formation of the heart, congenital cardiac malformations, and the phylogeny of the venous tributaries.