These scripts are based on the descriptions from the following paper:
"Quantitative assessment of the retinal microvasculature using optical coherence tomography angiography". Journal of Biomedial Optics, 21(6), 066008. 2016. Zhongdi Chu; Jason Lin; Chen Gao; Chen Xin; Qinqin Zhang; Chieh-Li Chen; Luis Roisman; Giovanni Gregori; Philip J. Rosenfeld; Ruikang K. Wang
Link to paper
Dimensions {x, y. z} corresponds to [0], [1], [2] when workin with ITK arrays that uses those dimensions/directions (index, size etc.)
Read more about ITK at itk.org
- For input,
typemeans the file type associated withfilename. - The scrips make output filenames themselves by using the input filename and append useful information about what happened.
- If the program runs with more arguments than specified, the program will
EXIT_FAILURE. - If the program runs with less arguments than specified, default arguments will be ran.
Complete/Abandoned. Implementing adaptive threshold filter. Abandoned because underlying filter is deprecated and suspect not implementing adaptive threshold correctly
Complete/Abandoned. Implementing the white hat filter, bringing out local maxima of bright objects on dark background. The filter isn't working correctly, output remained the same as input.
Arguments: ./WhiteHatThreshold [filename] [filetype] [algorithm] [radius]
Default: ./WhiteHatThreshold volume_norm_tif .nii 0 8
Complete. Micro script on MATLAB to make use of its adaptive thresholding and image binarizing functions. Playing around with parameters currently gives neighborhood sizes of [1 1 1] very effective.
Arguments: No arguments
Author: Viet Than, Department of EECS, Vanderbilt University, US.
Supervisor: Ipek Oguz, Prof. Department of EECS, Vanderbilt University, US.
With the help of the Medical Image Computing Lab.