3D Quantification of Vascular-Like Structures in z Stack Confocal Images

Ulrich Bonda; Anna Jaeschke; Anthony Lighterness; Jeremy G. Baldwin; Carsten Werner; Elena de Juan Pardo; Laura J. Bray

doi:10.1016/j.xpro.2020.100180

3D Quantification of Vascular-Like Structures in z Stack Confocal Images

Ulrich Bonda, Anna Jaeschke, Anthony Lighterness, Jeremy G. Baldwin, Carsten Werner, Elena de Juan Pardo, Laura J. Bray

Mechanical Engineering

Research output: Contribution to journal › Article › peer-review

7 Citations (Scopus)

Abstract

Optical slice microscopy is commonly used to characterize the morphometric features of 3D cellular cultures, such as in vitro vascularization. However, the quantitative analysis of those structures is often performed on a single 2D maximum intensity projection image, limiting the accuracy of data obtained from 3D cultures. Here, we present a protocol for the quantitative analysis of z stack images, utilizing Fiji, Amira, and WinFiber3D. This protocol facilitates the in-depth examination of vascular-like structures within 3D cell culture models. For complete details on the use and execution of this protocol, please refer to Koch et al. (2020).

Original language	English
Article number	100180
Number of pages	15
Journal	STAR Protocols
Volume	1
Issue number	3
DOIs	https://doi.org/10.1016/j.xpro.2020.100180
Publication status	Published - 18 Dec 2020

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10.1016/j.xpro.2020.100180Licence: CC BY-NC-ND

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title = "3D Quantification of Vascular-Like Structures in z Stack Confocal Images",

abstract = "Optical slice microscopy is commonly used to characterize the morphometric features of 3D cellular cultures, such as in vitro vascularization. However, the quantitative analysis of those structures is often performed on a single 2D maximum intensity projection image, limiting the accuracy of data obtained from 3D cultures. Here, we present a protocol for the quantitative analysis of z stack images, utilizing Fiji, Amira, and WinFiber3D. This protocol facilitates the in-depth examination of vascular-like structures within 3D cell culture models. For complete details on the use and execution of this protocol, please refer to Koch et al. (2020).",

keywords = "3D analysis, In vitro model, vascular",

author = "Ulrich Bonda and Anna Jaeschke and Anthony Lighterness and Baldwin, {Jeremy G.} and Carsten Werner and {de Juan Pardo}, Elena and Bray, {Laura J.}",

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doi = "10.1016/j.xpro.2020.100180",

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AU - Bonda, Ulrich

AU - Jaeschke, Anna

AU - Lighterness, Anthony

AU - Baldwin, Jeremy G.

AU - Werner, Carsten

AU - de Juan Pardo, Elena

AU - Bray, Laura J.

PY - 2020/12/18

Y1 - 2020/12/18

N2 - Optical slice microscopy is commonly used to characterize the morphometric features of 3D cellular cultures, such as in vitro vascularization. However, the quantitative analysis of those structures is often performed on a single 2D maximum intensity projection image, limiting the accuracy of data obtained from 3D cultures. Here, we present a protocol for the quantitative analysis of z stack images, utilizing Fiji, Amira, and WinFiber3D. This protocol facilitates the in-depth examination of vascular-like structures within 3D cell culture models. For complete details on the use and execution of this protocol, please refer to Koch et al. (2020).

AB - Optical slice microscopy is commonly used to characterize the morphometric features of 3D cellular cultures, such as in vitro vascularization. However, the quantitative analysis of those structures is often performed on a single 2D maximum intensity projection image, limiting the accuracy of data obtained from 3D cultures. Here, we present a protocol for the quantitative analysis of z stack images, utilizing Fiji, Amira, and WinFiber3D. This protocol facilitates the in-depth examination of vascular-like structures within 3D cell culture models. For complete details on the use and execution of this protocol, please refer to Koch et al. (2020).

KW - 3D analysis

KW - In vitro model

KW - vascular

U2 - 10.1016/j.xpro.2020.100180

DO - 10.1016/j.xpro.2020.100180

M3 - Article

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SN - 2666-1667

VL - 1

JO - STAR Protocols

JF - STAR Protocols

IS - 3

M1 - 100180

ER -

3D Quantification of Vascular-Like Structures in z Stack Confocal Images

Abstract

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