CBI Demo OPT

Author: François Marelli francois.marelli@idiap.ch, April 2023

Editor, supervision: Michael Liebling michael.liebling@idiap.ch

Overview

This repository contains a demo application for Optical Projection Tomography.

It uses a stepper motor controlled by Arduino to acquire different projections using a webcam, and reconstructs the images using FBP.

Example deployment

The demo as deployed in the Imaging Pavillion at the 2023 EPFL OpenDays on 29–30 April 2023.

Install instructions

Set up computer (macOS)

• install mambaforge
• install homebrew
• brew install git
  • brew install cmake
  • brew install openmp
  • brew install libomp
  • brew install gcc
  • conda install -c conda-forge clang_osx-65 issue: concorde does not install
• Should start install Xcode
• Install Logitech G HUB – Logitech Support + Download to set webcam focus to fixed setting

Python Environment

In order to use this demo, you need an environment with Python >= 3.5 and < 3.10.

mamba create -n demo_opt "python<3.10"
mamba activate demo_opt

Then install the package:

pip install .

Hardware setup

This demo uses a stepper motor controlled by Arduino. See https://github.com/idiap/arduino_pytwister for the firmware and wiring instructions.

1. Download the arduino firmware code

   git archive --remote=https://github.com/idiap/arduino_pytwister.git HEAD ArduinoPyTwisterFirmware/ArduinoPyTwisterFirmware.ino | tar -x

2. Connect arduino to USB port.

3. Open Arduino IDE software

4. Upload ArduinoPyTwisterFirmware.ino

You must set the rotating sample in front of a camera, and provide correct lighting.

Running the demo

First, list the available camera connected to the computer:

demo-opt list-cameras

Run the demo and provide either the name or the index of the camera of your choice:

# Using the camera's name
demo-opt run --camera-name "<CAMERA NAME>"
# Using the camera's index
demo-opt run --camera-index <INDEX>

While the demo is running, use the following key bindings to interact:

• Space: launch new acquisition/reconstruction
• Return: reset demo (discard acquired images)
• Escape: quit the demo