DORMOUSE: Detection Of Reflected Microscopic Optical UltraSound Emission

by Kenton Kwok, Yuji Go

part of Year 3 BSc Project, Department of Physics, Imperial College London

This is the GitHub repository of our BSc project under the supervision of Dr Chris Rowlands (Bioengineering, Imperial College London). We use a computer simulation approach to improve the understanding of a problem in an optics laboratory.

Projection Mechanism

Mainly worked on by Kenton

This is a k-Wave simulation to investigate the feasibility of a particular setup used for all-optical ultrasound generation. In particular we are concerned with a phased-array implementation of ultrasound scanning.

Two k-Wave simulations exist and are in MATLAB code. Running them requires the k-Wave simulation files which can be downloaded here.

• simulations/twod_scan.m which looks at the degradation of resolution
• simulations/twod_phantom.m which looks at the image performance when the waves are directed into a scattering phantom

They are based on the same example code by Treeby et. al. We could not use the default transducer MATLAB object provided as it did not give us the flexibility to modify the time delays. The result was to calculate the input signals and delay them externally.

The reset of the files are to do with analysis and plotting graphs

• analysis/basic.ipynb concerns simple plots for the project report
• analysis/image.ipynb concerns making plots of the phantoms
• analysis/analysis.ipynb is the main file and concerns the investigation of resolution and plotting figures

The analysis files will refer to raw .mat data files obtained using MATLAB but they have not been uploaded due to large file size.

The phantoms folder contains

• the ultrasound images used
• ImageJ ROI .zip files for annotation and analysis
• Excel files for analysis of the contrast

Two gifs are also uploaded in the videos folder for illustration

Detection Mechanism

Mainly worked on by Yuji