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Published November 2, 2020 | Version v1
Dataset Open

I2K2020 Data for "Quantification of the 3D brain vasculature in zebrafish light sheet fluorescence microscopy data"

  • 1. University of Sheffield

Description

Example data for the I2K2020 tutorial "Quantification of the 3D brain vasculature in zebrafish light sheet fluorescence microscopy data" (https://www.janelia.org/you-janelia/conferences/from-images-to-knowledge-with-imagej-friends/virtual-workshop-program)

"Readme" file for data description included in folder.

Background: Zebrafish transgenic lines and light sheet fluorescence microscopy (LSFM) allow unrivalled insights into vascular development in vivo and 3D. The vascular architecture can be used to describe physiological status. However, assessment of the vasculature still relies on individual visual assessment rather than objective quantification. Thus, an image analysis pipeline is required to allow data assessment in 3D robustly and sensitively, while being able to handle LSFM data.

Kugler et al have produced an image analysis workflow to quantify the zebrafish brain vasculature in 3D (https://www.biorxiv.org/content/10.1101/2020.08.06.239905v2).

Aim: In this tutorial we will use the analysis workflow produced by Kugler et al to examine and quantify the zebrafish brain vasculature in 3D with a hands-on practical (https://github.com/ElisabethKugler/ZFVascularQuantification).

Files

I2KData512x512.zip

Files (1.6 GB)

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Additional details

Related works

Is supplement to
Software: 10.5281/zenodo.3978278 (DOI)
Preprint: 10.1101/2020.08.06.239905 (DOI)
Dataset: 10.5281/zenodo.4108660; (DOI)