Scripts & Raw data - developmental staging of zebrafish embryos based on intra-nuclear distances

Scripts & microscopy image data required for the generation of a developmental staging chart for blastula stage zebrafish embryos. The generated staging chart allows using inter-nuclear distances as a marker for developmental progress.

This repository contains the script ProcessTimeLapse.m to process the raw .czi files obtained with a Zeiss Lightsheet microscope. The raw data are not contained, due to excessive file size of >700 GB, but can be obtained upon request. The second script NearestNeighborStaging_Calibration.m processes files obtained with the first script so as to provide the nearest-neighbour distances between nuclei over time. The intermediate .mat files are provided in this repository, so that this step of the analysis can be fully reproduced.

To carry out the analysis, the Open Microscopy Environments BioFormats plugin bfmatlab must be added to the MatLab path. Additional monitoring of parallel processing progress is provided via the parfor_progress.m function.