The application workflow starts by importing the original image files in arivis Pro. For each staining/hybridization cycle the new SIS file will be created. All Z planes from all the tiles will be imported separately into a single stack (single imageset). The import step is optional. Alternatively, the user can start the registration workflow by simply opening the already stored SIS files.

The registration workflow starts from creating the new SIS file to store the registration results. The first cycle image (fixed) will be identified automatically based on the filename. This image will remain untransformed. The 3D stack for each subsequent cycle (moving) will be transferred as new channels in the corresponding tile in the registered image file. The number of tiles should be consistent for all staining cycles.