Arduino implementation of ALEX (Alternating Laser Excitation) to synchronize illumination of two diode lasers with the exposure of an EMCCD camera in an interleaved manner.
This is the source code repository for the Arduino-ALEX firmware. The firmware was initially designed and used for:
Q: What is ALEX?
A: Refer to Kapanidis AN, Laurence TA, Lee NK, Margeat E, Kong X, Weiss S. Alternating-laser excitation of single molecules. Acc Chem Res. 2005.
Q: Why DIY ALEX using Arduino?
A: Most camera-based fluorescence microscopes are equipped with EMCCD and diode lasers, which can be digitally modulated. However, electronics to synchronize these components are not always available to the end user and could cost thousands of USD. In this implementation, the FIRE signal TTL (high) from the EMCCD is used to switch on the laser for a certain on-time (user-defined), bypassing the need for external clocking using an Arduino board (costing less than a hundred USD).
Q: How do I use the source code?
A: You will need to assemble the Arduino board, install the firmware, and follow the instructions provided in this repository.
The code is licensed under the GNU General Public License (GPL) so you are not required to cite this repository in the academic sense but it is good academic practice to cite the repo or at least acknowledge it especially if it significantly influenced your work. However you do have legal obligations if you distribute or modify the code. If you do happen to:
- Include the original license (e.g., LICENSE file).
- Include the copyright notice of the original author(s).
- Disclose your own source code if you distribute the combined/modified work.
- Ideally, acknowledge the original repo in your README or documentation, e.g., This project uses code from Arduino-ALEX, licensed under the GNU General Public License v3.0.