Scripts & Raw data - developmental staging of zebrafish embryos based on intra-nuclear distances
Year: 2023
Type: dataset
Abstract: 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.
Authors: Hilbert, Lennart, Vastenhouw, Nadine
Institutions: Karlsruhe Institute of Technology, University of Lausanne
Language: English
Subfield: Cell Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4393701877