Example Data for 3D quantification of zebrafish cerebrovascular architecture

Example data for: E. C. Kugler, J. Frost, V. Silva, K. Plant, K. Chhabria, T. J.A. Chico, P. A. Armitage 3D quantification of zebrafish cerebrovascular architecture by automated image analysis of light sheet fluorescence microscopy datasets bioRxiv 2020.08.06.239905; doi: https://doi.org/10.1101/2020.08.06.239905 Link: https://www.biorxiv.org/content/10.1101/2020.08.06.239905v2 <br> Code: https://github.com/ElisabethKugler/ZFVascularQuantification (doi:https://doi.org/10.5281/zenodo.3978278) 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. 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