A protocol and graphical user interface to assist new users with the planning of X-ray computed tomography experiments

Abstract

X-ray computed micro tomography (CT) is the main 3D technique for imaging the internal microstructures of samples. Experimental planning is crucial to ensure the adequacy of CT results to answer specific scientific questions, optimizing the use of resources and maximizing the quality of results. Proper planning requires a certain level of expertise in the technique and the details of the specific scientific question to be answered. Notably, potential new CT users who have formulated a scientific question may not have the in-depth knowledge about CT necessary to make a first assessment of whether CT is suitable for their work. Here, a step-by-step protocol to plan CT experiments and an interactive graphical user interface (XCT-Explorer) are proposed to guide users through the different steps of the protocol and to link the various CT parameters required to perform a scan. The protocol is based on the experience gained within EXCITE (Electron and X-ray microscopy Community for structural and chemical Imaging Techniques for Earth materials) through interactions between facility managers and users from various scientific fields. The planning protocol aims to 1) help potential CT users with limited knowledge of CT (e.g. first-time users) to decide whether CT can answer their scientific question; 2) guide users to decide which parameters are the most appropriate for their sample/problem; 3) facilitate the initial contact between CT provider and new users; and 4) standardize the planning stage of CT experiments as the foundation for FAIR (Findable Accessible Interoperable and Reusable) practices.