OpenOPTI (A cheap open-source 3D Microscope)

Optical Projection Tomography (OPT) uses similar reconstruction methods as CT x-ray imaging but with visible light for microscoping samples. By taking hundreds of pictures of a sample from every angle of rotation, a 3D representation of that sample can be obtained with the focus and clarity of traditional microscopes without the need for destructive physical sectioning.

There are many ways of doing this, however in the name of simplicity and frugality I went with the most basic approach here to start with, resulting in a performant device that costs roughly $60. The rig consists of: a USB microscope ($20), mirror ($1), stepper motor ($15), EasyDriver stepper motor driver($7), 10W LED ($8), variable buck-converter ($2), Arduino Nano ($4), and small AC/DC power supply ($5).

Matlab code is here: https://drive.google.com/file/d/1b-BmD_G1TKKAKyeW1MWYgqi3KEwDDZLn/view?usp=share_link 

The matlab code does an incredible amount of the lifting here, and it does everything with 1 click, from acquisition to the actual projection computations. Provided your sample is properly aligned in the image frame, this should yield fairly good results right away once you set your thresholds in the visualizer. 

Steps to run:

1. Install the arduino firmware
2. Install the Matlab CT Reconstruction Package Add-on (https://www.mathworks.com/matlabcentral/fileexchange/35548-3d-cone-beam-ct--cbct--projection-backprojection-fdk--iterative-reconstruction-matlab-examples)
3. Change the COM port in the Matlab script to your Arduino's current port.
4. Enable or disable CUDA in the Matlab script if you don't have an Nvidia graphics card
5. Center and focus your sample of choice exactly in the center of the camera's frame.
6. Click Run.
7. Wait awhile
8. Turn on Volume 1
9. Turn on a Rendering setting
10. Threshold the resulting 3D rendering until you get only the bits of the reconstruction that you want

I've posted this here in hopes that someone somewhere can get some enjoyment or better yet productive use from having a cheap 3D microscope. If that's you and you have comments or questions please feel free to contact me here in the comments section and I'll do my best to help.