bu-cisl/IDT-using-Annular-Illumination — reverse-engineered prompt

Build me a MATLAB demo project for annular illumination intensity diffraction tomography, based on the high speed in vitro IDT paper. I want to be able to put the raw microscope data in the same folder, choose one of the sample demos, and run one main script to reconstruct a 3D refractive index volume from a small set of intensity images.

Please include separate runnable demos for diatom samples, cheek cell clusters, and cropped C elegans data. The workflow should handle setup, calibration, illumination position sorting, reconstruction, and display of the final tomography results. It should save useful figures so I can compare the output with the paper images.

Keep it compatible with MATLAB R2018a if possible. Make the code organized into clear functions and utilities, with comments explaining the steps in plain language. Add a short README that tells me where to download the raw data, where to place it, and exactly which script to run for each demo.