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

<p>Scripts &amp; 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.</p> <p>This repository contains the&nbsp;script <em>ProcessTimeLapse.m</em> to process the raw <em>.czi</em> files obtained with a Zeiss Lightsheet microscope. The raw data are not contained, due to excessive file size of &gt;700 GB, but can be obtained upon request. The&nbsp;second script&nbsp;<em>NearestNeighborStaging_Calibration.m</em> processes files obtained with the first script so as to provide the nearest-neighbour distances between nuclei over time. The intermediate <em>.mat</em> files are provided in this repository, so that this step of the analysis can be fully reproduced.</p> <p>To carry out the analysis, the Open Microscopy Environments&nbsp;BioFormats plugin <em>bfmatlab</em> must be added to the MatLab path. Additional monitoring of parallel processing progress is provided via the <em>parfor_progress.m</em> function.</p>