Advance in technology brings new challenges and possibilities in various fields, including medicine. The novel technology is capable of supporting domain experts (DE) in their daily routine and speeding up the classification work. This study proposes a modified Domain-Expert-Centred Double Diamond design (DEDDM) methodology to optimise the interaction between DE and technology innovations in the field of histopathology through an innovative interface design. To achieve a good user experience (UX) and usability, the DEDDM methodology was built around the specific needs of DE in the field of histopathology in a time-efficient form, due to the high workload of DE. The proposed DEDDM methodology was validated in a case study for the user interface design of a tool to assist histopathologists in the Primary ciliary dyskinesia (PCD) diagnostics. As a result of the validation, a high-fidelity prototype of a medical imagery annotation tool for PCD is presented. The prototype was iteratively evaluated and refined during user testing sessions. The presented case study points towards the feasibility of the DEDDM methodology for designing annotation interfaces in the medical domain and demonstrates the usefulness of the modified design process for further use in the user interface design for the medical domain.