Use of ‘reference series’ to realign histological serial sections for three-dimensional reconstructions of the positions of cellular events in the developing brain

Knabe, Wolfgang; Washausen, Stefan; Brunnett, Guido; Kuhn, Hans-Jürg

doi:10.1016/s0165-0270(02)00247-9

Cited by 26 publications

(36 citation statements)

References 31 publications

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“…This method is especially suitable for reconstructing small embryos in utero as well as genetically modified and potentially malformed embryos which may lack relevant internal fiducial markers, e.g., symmetrically aligned organ rudiments and/or midline structures (Fig. 16, Knabe et al, 2002).…”

Section: -D Reconstruction Techniquesmentioning

confidence: 99%

Early development of the nervous system of the eutherian <i>Tupaia belangeri</i>

Knabe¹,

Washausen²

2015

Primate Biol.

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Abstract. The longstanding debate on the taxonomic status of Tupaia belangeri (Tupaiidae, Scandentia, Mammalia) has persisted in times of molecular biology and genetics. But way beyond that Tupaia belangeri has turned out to be a valuable and widely accepted animal model for studies in neurobiology, stress research, and virology, among other topics. It is thus a privilege to have the opportunity to provide an overview on selected aspects of neural development and neuroanatomy in Tupaia belangeri on the occasion of this special issue dedicated to Hans-Jürg Kuhn. Firstly, emphasis will be given to the optic system. We report rather "unconventional" findings on the morphogenesis of photoreceptor cells, and on the presence of capillary-contacting neurons in the tree shrew retina. Thereafter, network formation among directionally selective retinal neurons and optic chiasm development are discussed. We then address the main and accessory olfactory systems, the terminal nerve, the pituitary gland, and the cerebellum of Tupaia belangeri. Finally, we demonstrate how innovative 3-D reconstruction techniques helped to decipher and interpret so-far-undescribed, strictly spatiotemporally regulated waves of apoptosis and proliferation which pass through the early developing forebrain and eyes, midbrain and hindbrain, and through the panplacodal primordium which gives rise to all ectodermal placodes. Based on examples, this paper additionally wants to show how findings gained from the reported projects have influenced current neuroembryological and, at least partly, medical research.

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Section: -D Reconstruction Techniquesmentioning

confidence: 99%

Early development of the nervous system of the eutherian <i>Tupaia belangeri</i>

Knabe¹,

Washausen²

2015

Primate Biol.

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“…Having established the high resolution scanning system Huge image [25] as well as new methods for the alignment of histological serial sections [16] and for the triangulation of large embryonic surfaces [7,18], we have applied three-dimensional reconstruction techniques to identify new patterns and functions of programmed cell death (apoptosis) in the developing midbrain [15], hindbrain [17], and in the epibranchial placodes [29].…”

Section: Introductionmentioning

confidence: 99%

A Framework for the Visualization of Cross Sectional Data in Biomedical Research

Kienel

Vanco

Brunnett

et al. 2008

Mathematics and Visualization

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In this paper we present the framework of our reconstruction and visualization system for planar cross sectional data. Threedimensional reconstructions are used to analyze the patterns and functions of dying (apoptotic) and dividing (mitotic) cells in the early developing nervous system. Reconstructions are built-up from high resolution scanned, routinely stained histological serial sections (section thickness = 1 µm), which provide optimal conditions to identify individual cellular events in complete embryos. We propose new sophisticated filter algorithms to preprocess images for subsequent contour detection. Fast active contour methods with enhanced interaction functionality and a new memory saving approach can be applied on the pre-filtered images in order to semiautomatically extract inner contours of the embryonic brain and outer contours of the surface ectoderm. We present a novel heuristic reconstruction algorithm, which is based on contour and chain matching, and which was designed to provide good results very fast in the majority of cases. Special cases are solved by additional interaction. After optional postprocessing steps, surfaces of the embryo as well as cellular events are simultaneously visualized.

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“…The selection of 2-D registration criteria is important as individual sections are subject to independent geometric distortions and this can lead to an inaccuracies in the reconstructed 3-D volume if distortions are propagated. This accurate registration allows the creation of a "reference volume" [7]. The reference volume can be co-registered with the MR [2] or used solely to localise individual histological sections [7] by virtue of the fact that adjacent thin sections can be considered at the same position.…”

Section: Introductionmentioning

confidence: 99%

“…This accurate registration allows the creation of a "reference volume" [7]. The reference volume can be co-registered with the MR [2] or used solely to localise individual histological sections [7] by virtue of the fact that adjacent thin sections can be considered at the same position. Where it is not possible to create such a reference volume attempts have been made to combine the reconstruction and alignment in an iterative process [12].…”

Section: Introductionmentioning

confidence: 99%

2-D to 3-D Refinement of Post Mortem Optical and MRI Co-registration

Kenwright

Bardinet

Hojjat

et al. 2003

Lecture Notes in Computer Science

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Abstract. Accurate co-registration of MR images of the brain with pathological data from the same patient is required for many applications, including validation of in-vivo MRI processing. We present preliminary results from a 2-D optical to 3-D MRI registration process, which depends on initialisation using an initial 3-D reconstruction of post-mortem whole-brain or hemisphere slices from independent 2D images followed by 3-D to 3-D registration. Our overall approach progressively models the acquisition process, and the final stages account for variations in slice thickness and other errors that can occur as a result of the specimen preparation and earlier processing. Our method can be used in most neuropathology laboratories where thick slices are cut. Alternative approaches depend on sectioning by macrocryotomes, which are not generally available and have limited applicability in conditions such as CJD where infectivity risks are high.

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Use of ‘reference series’ to realign histological serial sections for three-dimensional reconstructions of the positions of cellular events in the developing brain

Cited by 26 publications

References 31 publications

Early development of the nervous system of the eutherian <i>Tupaia belangeri</i>

Early development of the nervous system of the eutherian <i>Tupaia belangeri</i>

A Framework for the Visualization of Cross Sectional Data in Biomedical Research

2-D to 3-D Refinement of Post Mortem Optical and MRI Co-registration

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Use of ‘reference series’ to realign histological serial sections for three-dimensional reconstructions of the positions of cellular events in the developing brain

Cited by 26 publications

References 31 publications

Early development of the nervous system of the eutherian &lt;i&gt;Tupaia belangeri&lt;/i&gt;

Early development of the nervous system of the eutherian &lt;i&gt;Tupaia belangeri&lt;/i&gt;

A Framework for the Visualization of Cross Sectional Data in Biomedical Research

2-D to 3-D Refinement of Post Mortem Optical and MRI Co-registration

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Early development of the nervous system of the eutherian <i>Tupaia belangeri</i>

Early development of the nervous system of the eutherian <i>Tupaia belangeri</i>