## 2 Materials and Methods  
### Apple Samples  
The commercial apple cultivar, Gala, from the United States was used. Those were purchased from a local market. The study comprises two experiments conducted at different times. Because of a prolonged time needed for the measurement by FDPM system, only six apple samples was used for each experiment. The apples in the first experiment were kept in an air-conditioned room, and the temperature and relative humidity were set to 25 \({}^{\circ}\)C and 60%, respectively. The apples in the second experiment were stored in the refrigerator, with a temperature and relative humidity of 4 \({}^{\circ}\)C and 30%, respectively. The apples in the refrigerator were kept in plastic bags to reduce water evaporation. The DRS measurements of the optical properties of each apple sample were performed \(1,7,\) and \(14\) days after purchase.  
Frequency-Domain Photon Migration (FDPM) Diffuse Reflectance Spectroscopy (DRS) System and Artificial Neural Network (ANN)  
The configuration of our FDPM DRS system is shown in Figure 1. Two laser diodes with wavelengths of 660 and 980 nm, corresponding to the chlorophyll-a and water absorption peaks, were used in the system. They were installed on laser diode mounts (LDM9T, Thorlabs, Newton, NJ, USA), and driven by RF signals generated from a network analyzer (N5230C, Agilent, Santa Clara, CA, USA) and a DC source (LDC-3908, ILX, St. Charleston, SC, USA) to produce an intensity-modulated light at 10 dBm sinusoidal RF power in the range of 10-500 MHz. The network analyzer swept through 201 frequency points that were equally spaced between the starting and stopping frequencies. The RF switch was programmed to direct the RF signal to one diode laser at a time. The diffuse reflectance of apples measured at a certain SDS was coupled to an avalanche photo detector (APD, C5658, Hamamatsu, Japan) to convert the RF signal feeding back to the network analyzer's receiver port. The amplitude data represent the ratio of the sample to reference signal amplitudes, while the phase data represent the phase difference between the sample and reference signals.  
The source and detector optical fibers used in the system were two-step index fibers with 440 \(\upmu\)m core size and NA of 0.37. The measured variables for the FDPM measurements include the amplitude and phase of the intensity-modulated light. In order to separate amplitude and phase changes due to the instrument response, the system must first be calibrated with a standard of known optical properties. Calibration measurements are performed on homogeneous silicon or liquid phantoms of known properties in order to determine the instrument response of the system. We measured 5 points at the relatively flat spot of each apple, and each point was close by. The horizontal translation of the source and detector fibers was precisely controlled by a translation stage of accuracy within 10 \(\upmu\)m. The SDS was set to 1 and 5 mm, to investigate the relatively superficial and deep regions of the apple, respectively. We used a second translation stage to provide the vertical translation of the source and detector fibers. This vertical translation of the fibers was initiated before the measurement point was changed, to ensure that the fibers would not scratch the apple skin during measurement point adjustment. A vertical translation was initiated to return the fibers to their original measurement position after measurement point adjustment.