4108660
doi
10.5281/zenodo.4108660
oai:zenodo.org:4108660
James Frost
The University of Sheffield
Vishmi Silva
The University of Sheffield
Karen Plant
The University of Sheffield
Tim Chico
The University of Sheffield
Paul Armitage
The University of Sheffield
Example Data for 3D quantification of zebrafish cerebrovascular architecture
Elisabeth Kugler
The University of Sheffield
doi:10.1101/2020.08.06.239905
doi:10.5281/zenodo.3978278
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
zebrafish
lightsheet
quantification
analysis
brain
vasculature
<p>Example data for:</p>
<p>E. C. Kugler, J. Frost, V. Silva, K. Plant, K. Chhabria, T. J.A. Chico, P. A. Armitage</p>
<p>3D quantification of zebrafish cerebrovascular architecture by automated image analysis of light sheet fluorescence microscopy datasets</p>
<p>bioRxiv 2020.08.06.239905; doi: https://doi.org/10.1101/2020.08.06.239905</p>
<p>Link: https://www.biorxiv.org/content/10.1101/2020.08.06.239905v2</p>
<p><br>
Code: https://github.com/ElisabethKugler/ZFVascularQuantification (doi:https://doi.org/10.5281/zenodo.3978278)</p>
<p>Transgenic zebrafish 3dpf: Tg(kdrl:HRAS-mCherry)s916<br>
Acquisition: Zeiss Z.1 light sheet microscope with a Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, sCMOS detection unit. <br>
Activated pivot scan, dual-sided illumination and online fusion; <br>
properties of acquired data are as follows: 0.7x zoom, 16bit image depth, 1920 x 1920px (approximately 0.33 x 0.33 µm) image size and minimum z-stack interval (approximately 0.5µm), <br>
561nm laser, LP560, and LP585.</p>
<p>Data: <br>
- tiff and MIPs<br>
- TF: pre-processed with Sato enhancement<br>
- TH: segmented with Otsu thresholding<br>
- 512x512: downsampled<br>
- Reg: intersample registration<br>
- analysis: folder for quantification</p>
Zenodo
2020-10-20
info:eu-repo/semantics/other
4108659
0.1
1603196819.137992
5944410896
md5:a04ea724a173015d8cd16ffcc5e1eb45
https://zenodo.org/records/4108660/files/TestData_KuglerEtAl_ZFVascQuantification.zip
public
10.1101/2020.08.06.239905
Is part of
doi
10.5281/zenodo.3978278
Has part
doi
10.5281/zenodo.4108659
isVersionOf
doi