Atom probe tomography and related methods probe the 3D architecture of a material. Which software tools microscopists use and how these tools are connected into work flows makes a substantial contribution to the accuracy and precision of a materials characterization experiment. Typically, the tools of a specific community adapt results and methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. Microscopists more and more realize that improving on reproducibility and curation of their research is a challenge when it comes to align with the FAIR data stewardship principles. Facing this global challenge, we are convinced that teaming up is useful. Here, we report the results and challenges that we faced with an inter-laboratory call for developing test cases for several types of atom probe software tools. The results support, why defining detailed recipes of software work flows and sharing of these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to more substantiated results.