A 3D Brillouin microscopy dataset of the in-vivo zebrafish eye

Published: 04-03-2020| Version 3 | DOI: 10.17632/n9mzxxmhdm.3
Hector Sanchez-Iranzo,
Carlo Bevilacqua,
Alba Diz-Muñoz,
Robert Prevedel


Herein, we share a representative 3D spectral dataset of a 48-52 hours post-fertilization (hpf) zebrafish embryo eye, obtained by Brillouin microscopy, an all-optical and non-contact technique that gives access to material properties through the process of Brillouin scattering. This dataset encompasses the crystalline lens as well as the different retinal layers.


Steps to reproduce

The dataset is organized in two folders, which contain the data for two 3D regions of the eye. Each folder contains all the camera images for the reference (named 'reference-[index]') and for the sample (named spectrum[index]x[um]y[um]z[um]). To analyze the dataset, one needs to unzip the 'Analysis code.zip' folder and the dataset ('fish1_left.zip' and/or 'fish1_right.zip' ). Then one needs to run the Matlab script 'BrillouinDataAnalysis' located inside the folder 'Analysis code'; a dialog box will ask the user to select the unzipped folder containing the images. The next steps are exemplified in the folder 'Screenshots' inside the 'Analysis code' folder. The script prompts the user to: -draw a rectangle enclosing the spectrum -outline the spectral axis -select the two Brillouin peaks and baseline region of the spectrum. Upon completion, the script saves the fitted spectral parameters, i.e. frequency shift (fShift), width (fWidth), and amplitude (countsAmplitude), in location specified by the user.