@benedictdiederich
The Tinker Challenge: 3D Refractive Index Tomography with openUC2 is an immersive project designed to push the boundaries of DIY microscopy by enabling participants to “see the hard-to-see.” While most biological specimens are naturally transparent, this challenge focuses on mapping their internal structures by measuring their 3D refractive index. By capturing how light interacts with and slows down through a sample, such as plankton or small organisms, you can reveal intricate details that remain hidden in conventional brightfield imaging. The challenge begins with the physical assembly of a sophisticated optical setup using the modular openUC2 cube system. Participants will build an off-axis interferometer that combines a reference laser beam with light passing through the specimen. A key hardware component is a motorized sample rotation stage, controlled by an ESP32, which allows the specimen to be imaged from multiple angles. This hardware foundation integrates lasers, beam splitters, kinematic mirrors, and a camera into a stable, reproducible scientific instrument. The project is structured into a logical two-stage roadmap to guide development. In the first stage, Absorption Tomography, you will start by recording intensity changes as the sample rotates and reconstructing the object using back-projection algorithms. Once this foundation is solid, you will progress to the full project goal: 3D Phase Tomography. This advanced stage involves capturing off-axis holograms at every angle and performing phase retrieval through Fourier filtering to extract the complex wavefront. Finally, you will develop a computational reconstruction pipeline using Python and specialized libraries like Chromatix and JAX. Instead of relying on simple visual snapshots, you will apply gradient descent and forward modeling to iteratively reconstruct the final 3D volume. By completing this challenge, you will master the intersection of open-source hardware, computational imaging, and 3D data visualization, all while contributing to a global community of open science and reproducible research.
Here we share the link to the work we have done up until now: