XuvTools: free, fast and reliable stitching of large 3D datasets

Emmenlauer, Mario; Ronneberger, Olaf; Ponti, Aaron; Schwarb, Patrick; Griffa, Alessandra; Filippi, Alida; Nitschke, Roland; Driever, Wolfgang; Burkhardt, Hans

doi:10.1111/j.1365-2818.2008.03094.x

Cited by 134 publications

(115 citation statements)

References 18 publications

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“…Although prevention is better than cure, to some extent artifacts can be removed by image processing operations such as (nonlinear) smoothing (21,22), deconvolution (20,23,24), shading correction (21,22), and morphological filtering (25)(26)(27). In applications requiring both high magnification and a large field of view, it is also often necessary to make montages (mosaics of images of partially overlapping fields), which calls for accurate image registration and stitching to avoid discontinuities (28)(29)(30).…”

Section: Image Preprocessingmentioning

confidence: 99%

Neuron tracing in perspective

2010

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The study of the structure and function of neuronal cells and networks is of crucial importance in the endeavor to understand how the brain works. A key component in this process is the extraction of neuronal morphology from microscopic imaging data. In the past four decades, many computational methods and tools have been developed for digital reconstruction of neurons from images, with limited success. As witnessed by the growing body of literature on the subject, as well as the organization of challenging competitions in the field, the quest for a robust and fully automated system of more general applicability still continues. The aim of this work, is to contribute by surveying recent developments in the field for anyone interested in taking up the challenge. Relevant aspects discussed in the article include proposed image segmentation methods, quantitative measures of neuronal morphology, currently available software tools for various related purposes, and morphology databases. ' 2010 International Society for Advancement of Cytometry

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Section: Image Preprocessingmentioning

confidence: 99%

Neuron tracing in perspective

2010

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“…This setup was used to scan axons throughout the whole thickness of the optic nerve. To obtain 3D reconstruction of the optic nerves, image stacks were stitched using the XuvTools42 software 58 and the resulting macro-stack was exported to the Imaris Software (Bitplane, Zurich, Switzerland) to create 3D projections. Individual axons were analyzed semi-automatically with the Filament Tracers' advanced manual tracing mode ('AutoDepth').…”

Section: Moreover Inflammation-inducing Agents Such As Zymosan or Pamentioning

confidence: 99%

Cell type-specific Nogo-A gene ablation promotes axonal regeneration in the injured adult optic nerve

et al. 2014

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Nogo-A is a well-known myelin-enriched inhibitory protein for axonal growth and regeneration in the central nervous system (CNS). Besides oligodendrocytes, our previous data revealed that Nogo-A is also expressed in subpopulations of neurons including retinal ganglion cells, in which it can have a positive role in the neuronal growth response after injury, through an unclear mechanism. In the present study, we analyzed the opposite roles of glial versus neuronal Nogo-A in the injured visual system. To this aim, we created oligodendrocyte (Cnp-Cre þ / À xRtn4/Nogo-A flox/flox ) and neuron-specific (Thy1-Cre tg þ xRtn4 flox/flox ) conditional Nogo-A knock-out (KO) mouse lines. Following complete intraorbital optic nerve crush, both spontaneous and inflammation-mediated axonal outgrowth was increased in the optic nerves of the glia-specific Nogo-A KO mice. In contrast, neuron-specific deletion of Nogo-A in a KO mouse line or after acute gene recombination in retinal ganglion cells mediated by adeno-associated virus serotype 2.Cre virus injection in Rtn4 flox/flox animals decreased axon sprouting in the injured optic nerve. These results therefore show that selective ablation of Nogo-A in oligodendrocytes and myelin in the optic nerve is more effective at enhancing regrowth of injured axons than what has previously been observed in conventional, complete Nogo-A KO mice. Our data also suggest that neuronal Nogo-A in retinal ganglion cells could participate in enhancing axonal sprouting, possibly by cis-interaction with Nogo receptors at the cell membrane that may counteract trans-Nogo-A signaling. We propose that inactivating Nogo-A in glia while preserving neuronal Nogo-A expression may be a successful strategy to promote axonal regeneration in the CNS.

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“…Z-stacks were collected at 1-or 2-min intervals on a thermostated Nikon spinning disk. Adjacent z-stacks were stitched with XuvTools (49). Nuclei were automatically tracked by using Imaris software (Bitplane).…”

Section: Methodsmentioning

confidence: 99%

Collective mesendoderm migration relies on an intrinsic directionality signal transmitted through cell contacts

Dumortier

Martin

Meyer

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

109

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Collective cell migration is key to morphogenesis, wound healing, or cancer cell migration. However, its cellular bases are just starting to be unraveled. During vertebrate gastrulation, axial mesendoderm migrates in a group, the prechordal plate, from the embryonic organizer to the animal pole. How this collective migration is achieved remains unclear. Previous work has suggested that cells migrate as individuals, with collective movement resulting from the addition of similar individual cell behavior. Through extensive analyses of cell trajectories, morphologies, and polarization in zebrafish embryos, we reveal that all prechordal plate cells show the same behavior and rely on the same signaling pathway to migrate, as expected if they do so individually. However, by using cell transplants, we demonstrate that prechordal plate migration is a true collective process, as isolated cells do not migrate toward the animal pole. They are still polarized and motile but lose directionality. Directionality is restored upon contact with the endogenous prechordal plate. This contact dependent orientation relies on E-cadherin, Wnt-PCP signaling, and Rac1. Importantly, groups of cells also need contact with the endogenous plate to orient correctly, showing an instructive role of the plate in establishing directionality. Overall, our results lead to an original model of collective migration in which directional information is contained within the moving group rather than provided by extrinsic cues, and constantly maintained in cells by contacts with their neighbors. This self-organizing model could account for collective invasion of new territories, as observed in cancer strands, without requirement for any attractant in the colonized tissue.embryogenesis | cell movement | 3D tracking

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XuvTools: free, fast and reliable stitching of large 3D datasets

Cited by 134 publications

References 18 publications

Neuron tracing in perspective

Neuron tracing in perspective

Cell type-specific Nogo-A gene ablation promotes axonal regeneration in the injured adult optic nerve

Collective mesendoderm migration relies on an intrinsic directionality signal transmitted through cell contacts

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