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Fourier transform infrared (FT-IR) spectra were obtained using a JASCO FT-IR 300E spectrometer (JASCO Inc., Easton, MD, USA) at a resolution of 4 cm-1.
The Fourier transform infrared spectra of the samples were measured on a BRUKER EQUINOX-55 Fourier transform infrared spectrometer (Bruker Optics, Billerica, MA, USA) at a resolution of 4 cm−1 using the KBr technique.
After bi-planar exposures were taken, each film was digitized with a Microtek Medi-6000 scanner (Microtek Lab Inc, Santa Fe Springs, CA, USA) at a resolution of 600 dpi.
We digitized the images using a Cobrascan CX812T scanner (Radiographic Digital Imaging, Torrance, CA, USA) at a resolution of 150 pixels/inch (59 dots/cm).
The mammographic films from both breasts were scanned with a Kodak LS85 Film Digitizer Eastman Kodak Companyy, Rochester, NY, USA) at a resolution of 98 pixels per inch.
Slides were scanned immediately after post-hybridisation washing using a Genepix 4000B microarray fluorescence reader (Molecular Devices, Sunnyvale, CA, USA) at a resolution of 10 μm.
LC MS data was acquired using a Shimadzu Prominence HPLC system (Shimadzu, Japan), coupled online to a LTQ Orbitrap Velos instrument (Thermo Fisher Scientific, MA, USA) set at a resolution of 30,000 (at m/z 400).
A total of 120 screening mammograms were selected from the Dutch breast cancer screening program and were digitized by using a laser digitizer suitable for medical applications (Lumiscan 85, Lumisys, Sunnyvale, CA, USA) at a pixel resolution of 50 µm.
Bone wafers were scanned via high-resolution in vivo micro-computed tomography (VivaCT40, Scanco, Southeastern, PA, USA) at an isotropic resolution of 17.5 m with 55 keV cone beam mode.
The quality control images were acquired via the GenePix 4200AL scanner (Molecular Devices, CA, USA) at a 10 micron resolution and quantified with the Imagene 8.0 software suite.
Array scans were acquired with a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) at a 5 uM/pixel resolution and features were extracted with the GenePix 6.1 software.
