A) DATASET: The dataset is available as .RAR files in 2 parts each. Make sure to unzip the files before executing the codes.

1. Fresh THz data: Mouse5B_Fresh.mat
2. Block THz data: Mouse5B_Block.mat

Dataset description:

1. ScanData: matrix with dimensions <y,x,t> representing the data of the THz scan. y and x are the positions of the scan where a signal was received while t is the 1024-point time-domain signal received at that position. Generally our basic imaging consists of looking at the maximum of the ScanData along the t-axis to get a 2D image with dimensions <x,y>.
2. xrange: physical positions of the x-axis in the scan in millimeters.
3. yrange: physical positions of the y-axis in the scan in millimeters.
4. trange: time-domain axis of the reflected signal at each point in picoseconds in case you wish to plot individual time-domain signals.
5. matrix: matrix with dimensions <y,x> representing the ground truth obtained by morphing the pathology results. IMPORTANT: The data should be flipped vertically before being used (see line 28 in Amplitude_EM).
6. matrix_key_number: vector with dimension <k_total> with the key number representation of the k_total regions within the sample.
7. matrix_key_tissue: matrix with dimensions <k_original,c>, where c corresponds to the length of the string. Each row corresponds to the name that was given to each region and it follows the same order given in matrix_key_number, i.e., the matrix_key_number = 1 for matrix_key_tissue = CANCER.

B) MAIN FILES:

1. Amplitude_MCMC: MCMC algorithm that utilizes the amplitude spectrum of the THz data.
2. Amplitude_EM: EM algorithm that utilizes the amplitude spectrum of the THz data.
3. Complex_MCMC: MCMC algorithm that utilizes the complex spectrum of the THz data.
4. Complex_EM: EM algorithm that utilizes the complex spectrum of the THz data.

C) HOW TO RUN:

1. Download all the files in the repository and save them in the same folder.
2. Unzip the data files and make sure their names match the description in part A.
3. Run one of the main files.
4. Select the directory where you would like to save the results.

D) CHANGES To make any changes to the files, please refer to the comments included in the scripts.

E) CONTACT INFORMATION Tanny Chavez Esparza email: [email protected]