This repo contains code for my masters thesis. Project is aimed to provide a solution of reducing motion artifacts in images acquired via Optical Coherence Tomography technique.
| File | Description |
|---|---|
| saccadesModeling.mlx | Contains info about how eye movements were modeled. |
| phantomModeling.mlx | Shows how to apply saccadic motion to test data. |
| metricsModeling.mxl | Investigates image quality metrics (terrible) behaviour. |
| projectTest.m | Contains use cases for project. |
| RegistrationObjective.m | Encapsulates objective function for image registration. |
| RegistrationProcedure.m | Loads experiment data from resources and performs registration. |
| SaccadeGenerator.m | Generates saccadic movement. |
| ScannigProcedure.m | Modeles scanning procedure and applies saccadic movement to given original 3D image. |
First, checkout project.
$ git clone https://github.com/merlinDM/oct-motion-correction.gitAdd project to Matlab search path:
>> cd '/path/to/project/';
>> addpath(pwd);Run the example:
>> run 'phantomModeling.mlx';In 2019a it's impossible to make animation in Live Scripts. To see original and distorted image use lines (Ctrl+C in command window to stop):
>> visualize3d(acquiredImageXFast, acquiredImageYFast);Registration procedure could be tested using
>> runtests('projectTest')Also see scripts.m.
Matlab 2019a with Image Processing Toolbox installed.
Matthias Schabel, 3D Shepp-Logan phantom project, /+thirdparty/+phantom3d/ https://www.mathworks.com/matlabcentral/fileexchange/9416-3d-shepp-logan-phantom
Dirk-Jan Kroon, FMINLBFGS: Fast Limited Memory Optimizer, /+thirdparty/+lbfgs/ https://www.mathworks.com/matlabcentral/fileexchange/23245-fminlbfgs-fast-limited-memory-optimizer
Some matrix functions by Dirk-Jan Kroon from Finite Iterative Closest Point, /+thirdparty/+dkroon/ https://www.mathworks.com/matlabcentral/fileexchange/24301-finite-iterative-closest-point
Deshan Yang, Gaussian Pyramid - Expand and Reduce routines 1D, 2D and 3D, /+thirdparty/+pyramid/ https://www.mathworks.com/matlabcentral/fileexchange/12037-gaussian-pyramid-expand-and-reduce-routines-1d-2d-and-3d
T. Mahmudi, R. Kafieh, H. Rabbani, data from their paper OCT data & Color Fundus Images of Left & Right Eyes of 50 healthy persons https://sites.google.com/site/hosseinrabbanikhorasgani/datasets-1/oct-fundus-right-left