Design and implementation of a database and program for 3D reconstruction from serial sections: A data‐driven approach

Verbeek, Fons J.; Huijsmans, Dionysius P.; Baeten, R. J. A. M.; Schoutsen, N. J. C.; Lamers, Wouter H.

doi:10.1002/jemt.1070300607

Cited by 49 publications

(33 citation statements)

References 14 publications

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“…The reconstructions were derived from an aligned stack of images (Verbeek et al, 1995), followed by conversion to a volume model (Verbeek and Huijsmans, 1998), which was used to generate rendered images.…”

Section: Three-dimensional Reconstructionsmentioning

confidence: 99%

Septation and valvar formation in the outflow tract of the embryonic chick heart

et al. 2001

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There is no agreement, in the chick, about the number of the endocardial cushions within the outflow tract or their pattern of fusion. Also, little is known of their relative contributions to the formation of the arterial valves, the subpulmonary infundibulum, and the arterial valvar sinuses. As the chick heart is an important model for studying septation of the outflow tract, our objective was to clarify these issues. Normal septation of the outflow tract was studied in a series of 60 staged chick hearts, by using stained whole-mount preparations, serial sections, and scanning electron microscopy. A further six hearts were examined subsequent to hatching. At stage 21, two pairs of endocardial cushions were seen within the developing outflow tract. One pair was positioned proximally, with the other pair located distally. By stage 25, a third distal cushion had developed. This finding was before the appearance of two further, intercalated, endocardial cushions, also distally positioned, which were first seen at stage 29. In the arterial segment, the aortic and pulmonary channels were separated by the structure known as the aortopulmonary septum. The dorsal limb of this septum penetrated the distal dorsal cushion, whereas the ventral limb grew between the remaining two distal cushions, both of which were positioned ventrally. The three distal endocardial cushions, and the two intercalated endocardial cushions, contributed to the formation of the leaflets and sinuses of the arterial roots. The two proximal cushions gave rise to a transient septum, which later became transformed into the muscular component of the subpulmonary infundibulum. Concomitant with these changes, an extracardiac tissue plane was formed which separated this newly formed structure from the sinuses of the aortic root. Our study confirms that three endocardial cushions are positioned distally, and two proximally, within the developing outflow tract of the chick. Key words: heart; chick; developmental biology; scanning electron microscopy; embryology; morphogenesisThere have been numerous descriptions concerning septation of the outflow tract of the heart in different vertebrate species. It remains difficult to correlate the findings between different species, and reports regarding septation within the same species are frequently conflicting. To an extent, these difficulties reflect the formidable task of interpreting three-dimensional relationships in a structure as complex as the developing heart, but some do represent real morphologic differences between species. A firm understanding of these differences remains important, both because of the clinical significance of cardiac malformations (Anderson and Becker, 1992), and the use of animal models to establish the mechanisms of normal and abnormal development. Regardless of the species being studied, there is also considerable confusion regarding the nomenclature of the segments within the outflow tract, and their corresponding cushions.The outflow tract of the heart connects the develop...

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Section: Three-dimensional Reconstructionsmentioning

confidence: 99%

Septation and valvar formation in the outflow tract of the embryonic chick heart

et al. 2001

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“…The disadvantage of sectioning is the loss of integrity in the third dimension; therefore, 3D reconstruction from serial sections has been developed to restore initial relations in the object under study (Verbeek, 1995). In recent years, a number of software packages for 3D reconstruction at the microscopical level have become available (Huijsmans et al, 1986;Verbeek et al, 1990Verbeek et al, , 1991 and applied to anatomy (Gras, 1984;Mercer et al, 1987;Campbell et al, 1992), developmental biology Salisbury et al, 1993;Verbeek et al, 1995), neurosciences (Mercer et al, 1987;Rydmark et al, 1992), histopathology (Yaegashi & Takahashi, 1990;Dinges et al, 1992;Zanen et al, 1993) and tumour biology in the present study.…”

Section: Discussionmentioning

confidence: 83%

Three‐dimensional reconstruction of colon carcinoma metastases in liver

Griffini

Smorenburg

Verbeek

et al. 1997

Journal of Microscopy

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SummaryResection of liver metastases in patients with colon cancer increases survival but success depends on removal of all tumour tissue. For this purpose, understanding of spatial relationships between metastases and liver architecture is essential. Because metastatic cancer growth is essentially a three-dimensional (3D) event, we decided to apply 3D reconstruction techniques to study these spatial relationships between metastases and liver structures such as blood vessels, stroma and the liver capsule (Glisson's capsule). Colon carcinoma metastases were experimentally induced in rat liver by injection of colon cancer cells (CC531) into the portal vein. Three weeks later, livers from these animals and control livers were removed and immediately frozen in liquid nitrogen. Thirty-seven to 110 consecutive sections were used for each 3D reconstruction of 26 metastases in eight livers. Contours of different structures were stained by (immuno)histochemical means, traced in each section and stored in a database. From the contour model, a volume model was generated. Among the 26 metastases, seven were found to grow distantly from the liver capsule. They were small and consisted of well-differentiated cancer cells that were totally surrounded by a basement membrane and stroma which was always connected with adjacent blood vessels of a portal tract. The remaining 19 metastases showed a more advanced pattern of development. Infiltration of poorly differentiated colon cancer cells progressed through the stroma at various sites and areas of direct contact between cancer cells and hepatocytes were frequently found. This type of outgrowth of cancer cells was only found when metastases had made contact with the liver capsule. However, some areas in sections of these advanced stages still resembled small metastases. On the basis of these findings, we conclude that stroma affects the differentiation pattern of cancer cells and has at least a dual role in tumour growth. On the one hand it limits invasion of cancer cells in the surrounding host tissue. On the other hand, stroma formation at the capsule, which consists mainly of granulation tissue, facilitates outgrowth of the tumours. Furthermore, our 3D reconstructions demonstrate the spatial heterogeneity of larger metastases and the importance of a 3D approach to understand growth and development of metastases in general and colon cancer metastases in the liver in particular.

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“…Indeed, three-dimensional reconstruction has a relatively long history in biology (Gaunt and Gaunt 1978) and even among some arthropod systematists, especially when personal computers enabled a switch from a tedious manual process to computer-assisted reconstruction (Huijsmans et al 1986;Winslow et al 1987;Verbeek et al 1995).…”

Section: Three-dimensional Reconstructionmentioning

confidence: 99%

Evolutionary phenomics and the emerging enlightenment of arthropod systematics

Deans

István

Wipfler‍

et al. 2012

Invert. Systematics

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Abstract. Published research on the diversity and evolutionary history of Arthropoda sets a high standard for data collection and the integration of novel methods. New phylogenetic estimation algorithms, divergence time approaches, collaborative tools and publishing standards, to name a few, were brought to the broader scientific audience in the context of arthropod systematics. The treatment of morphology in these studies, however, has largely escaped innovation. Lodes rich in characters too often go unexplored, phenotype concepts are published with inadequate documentation and the way observations are textualised leaves them inaccessible to a majority of biologists. We discuss these issues, using data from recent arthropod systematics publications, and offer several that stand to restore the broad utility of morphological data. Specifically, we focus on: (1) the potential of internal soft-part characters and how to integrate their observation into arthropod systematics projects through dissection and serial sectioning; (2) the importance of capturing observations in images, especially using relatively new approaches, like laser scanning confocal microscopy and three-dimensional reconstruction; and (3) the untapped potential of established knowledge representation methods, which may help make the descriptive components of arthropod systematics research more accessible to other domains.

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Design and implementation of a database and program for 3D reconstruction from serial sections: A data‐driven approach

Cited by 49 publications

References 14 publications

Septation and valvar formation in the outflow tract of the embryonic chick heart

Septation and valvar formation in the outflow tract of the embryonic chick heart

Three‐dimensional reconstruction of colon carcinoma metastases in liver

Evolutionary phenomics and the emerging enlightenment of arthropod systematics

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