<p dir="ltr">We present a new registration pipeline called muvis-align, which is based on the multiview-stitcher toolbox. Multiview-stitcher is an open-source modular toolbox developed for distributed and tiled stitching of2-3D data. This modular, powerful toolbox is used to develop a flexible registration pipeline including pre-and post-processing steps as well as custom functions allowing x-y stitching and z reconstruction, for different image modalities. Importantly muvis-align overcomes limitations in existing tools used commonly, in particular handling large datasets (TBs) and fully supports the Next Generation File Format OME-Zarr. Preliminary registration tests show results of various LM and EM datasets equal or better compared to existing tools using affine transformations. This tool is further being developed with a napari user interface allowing easy configuration, exploring responsive dynamic configuration and providing visual feedback on preliminary and final results.</p>