Erratum: ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains

Ronneberger, Olaf; Liu, Kun; Rath, Meta; Rueß, Dominik; Mueller, Thomas; Skibbe, Henrik; Drayer, Benjamin; Schmidt, Thorsten; Filippi, Alida; Nitschke, Roland; Brox, Thomas; Burkhardt, Hans; Driever, Wolfgang

doi:10.1038/nmeth1012-1031c

Cited by 3 publications

(4 citation statements)

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“…We have assigned brain nuclei to major brain regions including the olfactory epithelia, telencephalon, diencephalon, hypothalamus, mesencephalon, metencephalon, myelencephalon, white matter, and spinal cord by cross-atlas registration (Raj et al, 2018; Ronneberger et al, 2012; Wullimann and Mueller, 2005). In addition, cell nuclei were automatically detected from head scans of intact fish using a supervised learning approach with a random forest classifier.…”

Section: Resultsmentioning

confidence: 99%

“…Landmarks were manually marked on corresponding anatomical regions. The detected brain regions were derived from segmented volumes of the larval (4 dpf) reference fish from the ViBE-Z zebrafish brain atlas (Ronneberger et al, 2012), which was used for the primary registration onto one of our 5 dpf samples. Validation of region detection was performed by cross-referencing to a histology-based developmental brain atlas (Wullimann and Mueller, 2005) and manual segmentation was used to correct areas of inaccurate registration.…”

Section: Methodsmentioning

confidence: 99%

“…Manual segmentations were performed using the open-source software, ITK-SNAP version 3.4 (Yushkevich et al, 2006) (http://www.itksnap.org). The ViBE-Z database and atlas are publicly available (http://vibez.informatik.uni-freiburg.de/) (Ronneberger et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

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Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Ding

Vanselow

Yakovlev

et al. 2019

eLife

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Organismal phenotypes frequently involve multiple organ systems. Histology is a powerful way to detect cellular and tissue phenotypes, but is largely descriptive and subjective. To determine how synchrotron-based X-ray micro-tomography (micro-CT) can yield 3-dimensional whole-organism images suitable for quantitative histological phenotyping, we scanned whole zebrafish, a small vertebrate model with diverse tissues, at ~1 micron voxel resolutions. Micro-CT optimized for cellular characterization (histotomography) allows brain nuclei to be computationally segmented and assigned to brain regions, and cell shapes and volumes to be computed for motor neurons and red blood cells. Striking individual phenotypic variation was apparent from color maps of computed densities of brain nuclei. Unlike histology, the histotomography also allows the study of 3-dimensional structures of millimeter scale that cross multiple tissue planes. We expect the computational and visual insights into 3D cell and tissue architecture provided by histotomography to be useful for reference atlases, hypothesis generation, comprehensive organismal screens, and diagnostics.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Ding

Vanselow

Yakovlev

et al. 2019

eLife

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“…Similarly, comparative studies of MG features across organisms could add to our current knowledge about MG conservation. Lastly, we believe that data integration by registration will allow the establishment of a virtual retina atlas, similar to the zebrafish brain atlas, allowing activity mapping (Randlett et al, 2015) and co-localization analysis (Ronneberger et al, 2012). Ultimately, collating and integrating descriptive modeling data will allow the development of predictive modeling approaches.…”

Section: Suggestions For Further Analysismentioning

confidence: 97%

Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit

2023

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Glial cells are the support cells of the nervous system. Glial cells typically have elaborate morphologies that facilitate close contacts with neighboring neurons, synapses, and the vasculature. In the retina, Müller glia (MG) are the principal glial cell type that supports neuronal function by providing a myriad of supportive functions via intricate cell morphologies and precise contacts. Thus, complex glial morphology is critical for glial function, but remains challenging to resolve at a sub‐cellular level or reproducibly quantify in complex tissues. To address this issue, we developed GliaMorph as a Fiji‐based macro toolkit that allows 3D glial cell morphology analysis in the developing and mature retina. As GliaMorph is implemented in a modular fashion, here we present guides to (a) setup of GliaMorph, (b) data understanding in 3D, including z‐axis intensity decay and signal‐to‐noise ratio, (c) pre‐processing data to enhance image quality, (d) performing and examining image segmentation, and (e) 3D quantification of MG features, including apicobasal texture analysis. To allow easier application, GliaMorph tools are supported with graphical user interfaces where appropriate, and example data are publicly available to facilitate adoption. Further, GliaMorph can be modified to meet users’ morphological analysis needs for other glial or neuronal shapes. Finally, this article provides users with an in‐depth understanding of data requirements and the workflow of GliaMorph. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Download and installation of GliaMorph components including example data Basic Protocol 2: Understanding data properties and quality 3D—essential for subsequent analysis and capturing data property issues early Basic Protocol 3: Pre‐processing AiryScan microscopy data for analysis Alternate Protocol: Pre‐processing confocal microscopy data for analysis Basic Protocol 4: Segmentation of glial cells Basic Protocol 5: 3D quantification of glial cell morphology

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Three-Dimensional Histology of Whole Zebrafish by Sub-Micron Synchrotron X-ray Micro-Tomography

Ding

Vanselow

Yakovlev

et al. 2018

Preprint

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Histological studies providing cellular insights into tissue architecture have been central to biological discovery and remain clinically invaluable today. Extending histology to three dimensions would be transformational for research and diagnostics. However, three-dimensional histology is impractical using 45 current techniques. We have customized sample preparation, synchrotron X-ray tomographic parameters, and three-dimensional image analysis to allow for complete histological phenotyping using whole larval and juvenile zebrafish. The resulting digital zebrafish can be virtually sectioned and visualized in any plane.Whole-animal reconstructions at subcellular resolution also enable computational characterization of the zebrafish nervous system by region-specific detection of cell nuclei and quantitative assessment of 50 individual phenotypic variation. Three-dimensional histological phenotyping has potential use in genetic and chemical screens, and in clinical and toxicological tissue diagnostics. One Sentence Summary:Synchrotron X-ray micro-tomography can be used to rapidly create 3-dimensional images of fixed and stained specimens without sectioning, enabling computational histological phenotyping at cellular 55 resolution. Running Title:Whole zebrafish 3D histology by micro-CT

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Erratum: ViBE-Z: a framework for 3D virtual colocalization analysis in zebrafish larval brains

Cited by 3 publications

References 1 publication

Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography

Glia Cell Morphology Analysis Using the Fiji GliaMorph Toolkit

Three-Dimensional Histology of Whole Zebrafish by Sub-Micron Synchrotron X-ray Micro-Tomography

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