Microscopy-based assessment of RNA polymerase II clusters during early stages of zebrafish embryo development

This repository contains the data and MatLab analysis scripts of the analysis of RNA polymerase II clusters over the course of zygotic genome activation and gastrulation of zebrafish embryos. Samples were prepared and images were recorded by Irina Mamontova and Agnieszka Pancholi in Lennart Hilbert's laboratory, images were analyzed by Lennart Hilbert. To analyse date data, the raw image data are first extracted into MatLab-native files using the MultiPosition_extraction_nd2.m script. The actual analysis is then carried out using the ClusterAnalysis.m script. Example microscopy images were produced using the ExampleImages.m script. The extracted data can be reviewed using the ReviewExtractedStacks.m script. For the analysis of nuclear and Pol II cluster properties, the following script was used: ClusterAnalysis.m After the primary image analysis, the following MatLab workspace save file was created, which allows obtaining the final analysis results: StageFigure_IntermediateSave_28Sep2025.mat For the analysis of cluster volume and solidity over developmental stages, a different script with minimal cluster volume of 0.01 µm^3 was used: ClusterAnalysis_VolumeThreshold_0_01.m After the primary image analysis, the following MatLab workspace save file was created, which allows obtaining the final analysis results: ModelFigure_IntermediateSave_Vol0_01um_11Jan2026.matThe raw image data will be uploaded to additional Zenodo repositories, which will be linked here after completion of the uploads. The reserved DOIs are: 10.5281/zenodo.18436843 (Oblong, Sphere, Dome) https://doi.org/10.5281/zenodo.18436851 (30% Epiboly, 50% Epiboly) https://doi.org/10.5281/zenodo.18436843