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

Boer, Bouke A. de; Soufan, Alexandre T.; Hagoort, Jaco; Mohun, Timothy J.; Hoff, Maurice J.B. van den; Hasman, Arie; Voorbraak, Frans; Moorman, Antoon F.M.

doi:10.1242/dev.051086

Cited by 45 publications

(41 citation statements)

References 23 publications

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“…Here we present a novel digitized approach for high resolution 3D reconstructions of protein expression and vessel branching based on standard 2D sections [30-32]. The protocols developed are based on archival serial sectioned tissue samples applying state-of-the art image processing using Adobe Photoshop combined with the highly flexible software platform "Amira".…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2011

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

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Section: Resultsmentioning

confidence: 99%

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

et al. 2011

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“…Images were acquired with a confocal microscope (Leica TCS SPE) taking 10 optical sections per histological section. After acquisition, 3D reconstructions were performed as described previously 58 and the resulting surfaces were exported to Adobe Acrobat Professional 9 Extended version to generate 3D interactive pdf files 59 .…”

Section: Methodsmentioning

confidence: 99%

Sequential Notch activation regulates ventricular chamber development

et al. 2015

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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.

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“…To combine our 3D model with the cell lineage and anatomical data into one platform, we embedded the 3D objects into an Adobe Systems' Portable Document Format (PDF) file, a format widely used for the distribution of scientific papers (de Boer et al, 2011;Murienne et al, 2008;Ruthensteiner and Hess, 2008). The PDF version of 3DVMTE is advantageous for us to distribute anatomical information easily as well as to understand the complex anatomy.…”

Section: Annotating Cell Lineage and Anatomical Information To 3d Modelmentioning

confidence: 99%

Three-dimensional anatomy of the Ciona intestinalis tailbud embryo at single-cell resolution

Nakamura

Terai

Okubo

et al. 2012

Developmental Biology

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During embryogenesis, chordates pass through a tailbud stage in which the larval tail is formed. Since acquisition of a tadpole-like tail during tailbud stage is one of the key events in the evolution of chordates, understanding the anatomy of the tailbud stage chordate embryo is of special interest. In this study, to understand comprehensively the anatomy of the tailbud embryo at single-cell-level, real microscopic image stacks of the tailbud embryo in Ciona intestinalis were reconstructed into a 3D computer model. This comprehensive 3D model of the ascidian tailbud embryo was based on real images of confocal laser scanning microscope (CLSM) and therefore, cell shape, location and cell arrangement reflect real geometries of the tailbud embryo. We found that the tailbud embryo consists of 1579 cells, including 836 epidermal cells, 228 cells in the central nervous system, 218 mesenchymal cells, four trunk ventral cells, two B/B(⁎)8.11 cells, 36 muscle cells, 40 notochord cells, four primordial germ cells, and 199 endodermal cells. Moreover, we identified for the first time two populations of previously undefined cells (a total of 12 cells) in Ciona: one located in the lateral trunk and the other located under the tail dorsal epidermis. This information provides a first step for understanding how the body plan of the chordate tailbud embryo formed and evolved.

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

Cited by 45 publications

References 23 publications

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

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

Sequential Notch activation regulates ventricular chamber development

Three-dimensional anatomy of the Ciona intestinalis tailbud embryo at single-cell resolution

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