This repository contains the Tissue Optics app used as a support for computer exercises on light propagation in tissue during the Biophotonics Workshop organised by the Irish Photonic Integration centre (IPIC) and sponsored by Science Fundation Ireland.
A version of this app that works inside a web browser app can be found in the javascript folder. This version has been written in javascript and do not require any installation to run. To run it locally on your own computer you simply need the source code, and to run a local webserver. Alternatively, the app is also hosted on Github Pages: https://biophotonics-tyndall.github.io/GEN-TissueOpticsApp/
An executable file was packaged from the original matlab based app and can be found in the matlab folder. This executable do not require to have matlab installed on the computer, however, it requires installing Matlab Runtime, which is free. See README file in corresponding folder for installation instructions.
User manuals for the app can be found:
- https://www.researchgate.net/publication/343789233_Using_the_functions_and_subfunctions_of_the_tissue_optics_app_directly_from_MATLAB
- https://www.researchgate.net/publication/343789002_Tissue_optics_simulations
When using our tissue optics app or publishing your results based on the app, please cite:
- Nogueira, Marcelo Saito, et al. "User-friendly graphical user interface for simulating tissue optical properties and fluence rates: improving students learning in tissue optics." Proceedings of SPIE. Optical Interactions with Tissue and Cells XXXI. Vol. 11238. International Society for Optics and Photonics, 2020.
- Nogueira, Marcelo S., et al. "Method of continuous improvement of multidisciplinary programs and outreach activities." Education and Training in Optics and Photonics. Optical Society of America, 2019.
- Nogueira, Marcelo Saito, et al. "Teaching light-tissue interactions: using technology for education." Proceedings of SPIE. Optical Interactions with Tissue and Cells XXX. Vol. 10876. International Society for Optics and Photonics, 2019.
The original computer exercise was developed for a Biophotonics course at the University of Lund Sweden by Stefan Andersson-Engels, Tomas Svensson and Johan Axelsson.
The first graphic user interface of this app was developed using MATLAB for the Biophotonics workshop of the Biophotonics@Tyndall team in Cork by Jacqueline Gunther.
The web version of the app has been developed for a remote version of the Biophotonics workshop in Cork by Baptiste Jayet and Jean S. Matias.
Thank you to Marcelo Nogueira and Jacqueline Gunther for corrections and suggestions. We acknowledge the Biophotonics workshop organisers since 2018 for the feedback received to improve the app and for its promotion during the event.