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The HR-pQCT scans were analysed using a new method developed for this study: high resolution tissue classification (HRTC).
The 0 45 min dynamic PET scans were analysed using Casciari model to report hypoxia and perfusion.
The scans were analysed using Sedfit program [38].
Hip scans were analysed using the hip structural analysis (HSA) program (version 1) [26].
Digitally stored CT scans were analysed using Slice-O-Matic software V4.2 (Tomovision, Montreal, Canada).
The scans were analysed using PMOD 2.95 (PMOD Technologies Ltd., Zurich, Switzerland).
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The images obtained after scanning were analysed using Agilent Feature Extraction software v. 10.5.1.1.
The TIF images derived from the slide scanning were analysed using DArTsoft version 7.3 (Cayla et al. in preparation), a dedicated software package developed at DArT P/L which is available to DArT network members [ 27].
Every other scan was analysed using Sedfit Version 9.2, (20) using the continuous size distribution (c(s)) method entering no prior knowledge.
Scan data were analysed using GeneSpring GX v12 (Agilent Technologies, UK). Baseline transformation was not employed and data were normalised using a Lowess model.
The gel was visualised on a Typhoon 9410 scanner, the scanned gels were analysed using ImageQuant TL software (Amersham Biosciences, UK).
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