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Package name Macula Modeller and Scan Synchronizer
Language MATLAB
Author József Vass <jozsef.vass@outlook.com>
Project for Andrew Symons <andrewsymons@gmail.com>
Joos Meyer <joos.meyer@gmail.com>
Version date Jul. 2, 2021
MATLAB R2021a
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Purpose
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This software package was created to handle the following tasks:
▪ Importing the macula scan output files, given in a particular format, and converting them to layer matrices that can be analyzed in MATLAB, corresponding to the 11 standard layers of the retina.
▪ Visualizing the retinal layers in 3D.
▪ Modelling the 2D central cross-section of a macula scan with the Difference of Gaussians (DoG) model in the literature.
▪ Modelling the macula in 3D with the above model to find its most reasonable center and foveal radius.
▪ Transforming a batch of scans, often several visits for a particular patient, to a common mesh, i.e. shifting the foveal centers to the mesh center, and making the mesh dimensions a standard factor of the foveal radius.
Instructions for use
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1. Create a folder to work in. Unzip / move this package there.
2. Download and unzip the open source packages listed below.
3. Download, install, and launch MATLAB (trial version available).
4. Navigate to this package in your created folder with the "Browse for folder" icon towards the top-left of the MATLAB interface, so that you can see main.m in the left-sidebar of MATLAB.
5. Type "main" at the >> prompt, and hit enter. This will launch the software menu.
6. Always start with either option 1. for loading raw data (for further analysis via the other options), or 8. for processing raw data to a standard mesh (which automatically includes / runs several other menu options, like modelling).
Open source packages:
Download and unzip these packages under the Open_Source folder, so that the .m files are directly under the subfolder names below.
▪ cprintf:
https://www.mathworks.com/matlabcentral/fileexchange/24093-cprintf-display-formatted-colored-text-in-the-command-wind/
▪ export_fig:
https://www.mathworks.com/matlabcentral/fileexchange/23629-export_fig/
▪ fit_ellipse:
https://www.mathworks.com/matlabcentral/fileexchange/3215-fit_ellipse/
▪ hline_vline:
https://www.mathworks.com/matlabcentral/fileexchange/1039-hline-and-vline/
Input:
▪ The raw scan data files are to be placed under Data/xls. The Data/scans.xlsx file can be generated by this software, but the mesh parameters (increments A/Binc and size A/Bnum columns) should be filled in manually based on the scanner settings.
▪ The processed data parameters file Data/scans_p.xlsx is generated automatically for runtime use, so it should never be edited!
▪ For modelling 2D cross-sections only (not from standard scan files), place your image file under Imgs. It should contain solely the contours of the nerve fiber layer, and two flat layers including / near the basement membrane.
▪ The Initialization section of main.m can be edited to change some global constants for the data location etc. (rare use).
Output: To be found under Plots, or Data/xls_p or csv_p.
Subroutine dependency tree
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main Main program launching the menu, and calling the subroutines.
MyHexaColor Converts hexagesimal color code to MATLAB convention.
OptSel Prompts a selection from a text menu of options.
OptSel2 Prompts a selection from a numerical menu of options.
DataImport Imports raw / processed data files.
OptSel See above.
OptSel2 See above.
MyStr2Num The built-in str2num generalized to "n/a" values.
DataMissingValues Fills in missing values in the raw data via interpolation.
SurfSym Symmetrizes the NFL layer in the x-direction (A scans).
ModelAxis2D Estimates the axis of a cross-section giving the best symmetry.
MyFindPeaks The findpeaks function generalized to account for global extrema.
PlotLayer Plots a layer in 3D relative to another.
DataStats Calculates some statistics for the loaded data.
ImgImport Imports a cross-section image file from Imgs.
OptSel See above.
ModelAxis2D See above.
Model_DoG2D 2D modelling (optimization) of a cross-section with DoG.
Function_DoG2D 2D DoG function.
MyR2 Finds the coefficient of determination.
ModelAxis3D Estimates the axis of a layer.
ModelAxis2D See above.
FitCircle Fits a circle to a set of points in the 2D plane.
ModInt Computes the residue of a real number w.r.t. an interval.
Model_DoG3D_Ell 3D modelling of a layer with elliptical DoG.
Function_DoG3D_Ell Elliptical 3D DoG function.
MyR2 See above.
Model_DoG3D_Cir 3D modelling of a layer with circular DoG.
Function_DoG3D_Cir Circular 3D DoG function.
MyR2 See above.
DataModel Finds the center and radius of the raw data.
MyStr2Num See above.
DataMissingValues See above.
ModelAxis3D See above.
FitCircle See above.
Model_DoG3D_Cir See above.
MyFindPeaks See above.
DataTransform Transforms all the layers to a common grid.
DataExport Exports the transformed layers in the original and matrix format.
TabSep Unions cell elements with a tab separator.