## 2 Materials and Methods  
### Sample Preparation  
Fresh samples of animal feces from dairy cows, pigs, chickens, and sheep were collected from animal research facilities and farms at the Beltsville Agricultural Research Center (BARC), Agricultural Research Service, United States Department of Agriculture. All fecal samples consisted of fresh droppings, and for each species, four samples of about 40 to 80 g each from individual animals were collected into polypropylene containers of 100 mL using sterilized disposable spatulas. The feces of dairy cows, chicken, and pigs were collected from individually housed animals, while very fresh sheep droppings were collected from free-ranging animals (outdoors). Collected samples are immediately stored at \(-20\)\({}^{\circ}\)C, and later allowed to stand at least 30 min to acclimate to room temperature before being used for imaging. Amended soil (sandy loam) samples were obtained from BARC high tunnel facilities usually used to grow produce. First, the fecal samples from each animal species and the soil samples were placed on a non-fluorescent tray, with each sample weighing approximately 30-35 g and covering an area approximately 5 cm in diameter. Hyperspectral fluorescence line-scan images of the feces and soil samples were replicated four times. Second, to evaluate soil-feces mixture matrix, soil samples were placed into four Petri dishes: one contained only soil, two contained soil topped with aggregated feces particles (approximately 5 to 10 mm in size) from each of the four animal species, and one contained soil mixed randomly with finely-cut feces particles (less than 3 mm in size) from each of the four animal species. All four Petri dishes were scanned together in one pass for hyperspectral image acquisition/analysis, replicated four times.  
In addition, samples of animal-mannure-based compost aged for one, two, three, and four months were obtained from the BARC Composting Research Facility on 11 February 2016. The exposed outdoor compost piles had been created on 7 January 2016 (one month prior), 2 December 2015 (two months prior), 7 November 2015 (three months prior), and 7 October 2015 (four months prior), placed over bare earth in windows approximately 50 m long, 1.5 m wide, and 1 m high. In terms of species origin of the animal feces present, the compost was mainly derived from cow feces along with mixtures of feces from other animal species such as horse, pig, sheep, and chicken. Note that compost contains mixtures of landscape trimmings and animal feed/bedding materials as well as feces/manure, and that the exact makeup and quantity of animal-fecal species were not quantified in this investigation. From each aged compost window, approximately 3 kg of compost was shoveled out to one mixing bucket from each of five holes distributed along the length of the 50 m window, for a total of 15 kg to mix together to produce a representative batch of the aged compost. Immediately after the mixing, approximately 3 kg of each representative compost batch was placed into a plastic bag for storage at \(-20\)\({}^{\circ}\)C. The four bags of aged compost were allowed to stand at room temperature for at least 30 min before being used for the imaging study. Each of the four batches of aged composts was used to fill five individual Petri dishes, for an arrangement of 20 samples in Petri dishes (four aged compost batches, five dishes per batch) that were then scanned together in one pass for hyperspectral imaging. Images were acquired for a total of 80 compost samples in four sets of 20 Petri dishes (in 4 aged month \(\times\) 5 sample arrangement).