Dataset Open Access

Example Data for 3D quantification of zebrafish cerebrovascular architecture

Elisabeth Kugler; James Frost; Vishmi Silva; Karen Plant; Tim Chico; Paul Armitage

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:


Code: (doi:

Transgenic zebrafish 3dpf: Tg(kdrl:HRAS-mCherry)s916
Acquisition: Zeiss Z.1 light sheet microscope with a Plan-Apochromat 20x/1.0 Corr nd=1.38 objective, sCMOS detection unit. 
Activated pivot scan, dual-sided illumination and online fusion; 
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), 
561nm laser, LP560, and LP585.

- tiff and MIPs
- TF: pre-processed with Sato enhancement
- TH: segmented with Otsu thresholding
- 512x512: downsampled
- Reg: intersample registration
- analysis: folder for quantification

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