r-FTIR python code and chemical heat maps for Walker et al. Underwater caves preserve biochemical composition and histological structure in modern and fossil mammalian bones

FTIRM Processing Pipeline for Modern and Fossil Samples from the submerged caves in Mount Gambier, South Australia============ This project preprocesses reflectance Fourier Transform Infrared Microspectroscopy (FTIRM) data from uniform spatial samples collected across sections of cortical bone.It is a custom preprocessing step from the article: Underwater caves preserve biochemical composition and histological structure in modern and fossil mammalian bones -------------------------------------------------- FEATURES--------- Reads a single or set of directories of individual spectra and arranges them according to sample images.- Detects and omits samples contaminated with epoxy.- Calculates baseline-corrected amplitudes for a set of specified wavelengths.- Constructs specified ratio images between two specified wavelengths.- Completes a linear correlation of row-wise averages across those ratio images to determine radial gradients.- Samples average sub-endosteal-, mid-cortical-, and sub-periosteal-most sections of ratio images for future analysis. -------------------------------------------------- FILE STRUCTURE-------------- ftir_spec/├── readme.txt├── dependencies.txt├── script_analysis.ipynb├── script_example.ipynb├── script_functions.py├── resources/│ ├── dat_environments.csv│ ├── dat_orientation.csv│ ├── dat_ratios.csv│ ├── dat_wavelengths.csv│ └── samples/└── outputs/ -------------------------------------------------- Note: File inputs within 'ftir_spec/resources/samples/' are provided at request of the lead (corresponding) author. For data requests, contact Meg Walker ([e-mail]). See the README doc for further information