The field of image-based spatial omics has been growing rapidly over the last years, and new software tools are constantly being developed. One key challenge for core facilities supporting these novel technologies is to integrate these processing and analysis packages into existing analysis workflows, and specifically to make them interoperable with already existing programs. QuPath(1) is an open-source program that is well established for visualising and analysing of Whole Slide Imaging (WSI) data. Therefore, it is ideally suited to serve for spatial image data as well. We are outlining the design and creation of a so-called QuPath extension to allow running a novel spot detection algorithm Spotiflow(2) inside QuPath. (1) https://github.com/qupath/qupath(2) https://github.com/weigertlab/spotiflow