Shine Stacker is a focus stacking application for microscopy, macro photography, and computational imaging. The software supports input in JPEG, 8 and 16-bit TIFF, PNG, and most RAW formats. Output can be JPEG, 8 and 16-bit TIFF, and PNG. It processes hundreds of images in batch: aligns, balances, and stacks layers. Its modular architecture allows combining processing modules according to project needs. Includes final interactive retouching of the stacked image from individual frames. For programmers, it offers a Python API and Jupyter Notebook support.