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

Advancements in non-invasive surface and internal imaging techniques, along with computational methods, have revolutionized 3D visualization of organismal morphology. These breakthroughs not only enhance research and medical anatomical analysis, but also facilitate 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 3D scientific data through cinematic rendering. This versatile pipeline supports multi-scale visualizations, from tissue-level to whole-organism details across diverse living organisms and is adaptable to various imaging sources and platforms. Its modular design and customizable rendering scenarios, provided by detailed SmARTR networks in a free software environment, make it a powerful tool for 3D data analysis. Accessible to a broad audience, SmARTR serves as a valuable resource not only for multiple fields of research in life sciences but also for education, diagnosis, outreach, and artistic endeavors.