The SmARTR pipeline: A modular workflow for the cinematic rendering of 3D scientific imaging data

Advancements in noninvasive surface and internal imaging techniques, along with computational methods, have revolutionized 3D visualization of organismal morphology—enhancing research, medical anatomical analysis, and facilitating the preservation and digital archiving of scientific specimens. We introduce the SmARTR pipeline (Small Animal Realistic Three-dimensional Rendering), a comprehensive workflow integrating wet lab procedures, 3D data acquisition, and processing to produce photorealistic scientific data through 3D cinematic rendering. This versatile pipeline supports multiscale visualizations—from tissue-level to whole-organism details across diverse living organisms—and is adaptable to various imaging sources. Its modular design and customizable rendering scenarios, enabled by the global illumination modeling and programming modules available in the free MeVisLab software and seamlessly integrated into detailed SmARTR networks, make it a powerful tool for 3D data analysis. Accessible to a broad audience, the SmARTR pipeline serves as a valuable resource across multiple life science research fields and for education, diagnosis, outreach, and artistic endeavors.