Scripts for local SSIM analysis and Fourier ring correlation assessment to show how far the SNR of the image can be compromised to let n2v recover the SNR post-acquisition. Download “Raw images.zip” which contains the raw data. Images are recruited RNA polymerase II (Pol II Ser5P and Ser2P) in live sphere stage zebrafish embryos, visualized with antibody fragments (Fab) labelled with Janelia fluor 647. Download and unzip “Processed_images.zip” which contains the TIF images of Pol II Ser5P images and the corresponding n2v_processed images. Python script named “zebrafish_nuclei_photo.py” generates images that are single image planes and were acquired with different exposure times. Intensity scale from black to white adjusted to the 0.01-th and the 99.99-th percentile. Matlab script named “lowestSSIMPercentile4zebrafish.m” generates average SSIM values based on the 5% lowest local SSIM values of the 5% brightest pixels. Python script “FRC_zebrafish.py” calculates the effective resolution as determined by FRC analysis for low-quality images, reconstructed images, and high-quality images for the different exposure times. “spin_average.py” file contains a function that is used in “FRC_zebrafish.py”.