X-ray Small and Wide Scattering scanning microscopies have been adopted to inspect morphological and structural properties of collagen-based tissues at the atomic and nano scale 1 . Examples will be discussed on specific pathologies: o osteoarthritis of the hip, also named osteoarthrosis of the hip or coxarthrosis, which is a chronic degenerative disorder of the hip joint, causing growing articular pain that can bring the patient to lifestyle limitations until surgical intervention is needed 2 o keratoconus, a pathology affecting cornea, which causes progressive thinning of the stroma and consequently abnormal curvature, inducing irregular astigmatism and myopia, corneal fibrosis, and distortion of vision, due to the modification in the organization of the corneal collagen 3 o abdominal aortic aneurysm, that occurs in the major artery from the hearth that supplies blood to the abdomen, and popliteal aneurysm, that takes place in the legs, behind the knees, characterized by alteration of collagen structure into vessel's wall of the aneurysm tissues, heterogeneous grade of inflammation related to infiltrating cells and extracellular matrix changes, in particular disruption of elastic fibers, fibrosis and calcifications 4 o diabetes mellitus, a metabolic disorder characterized by high blood sugar levels over a prolonged period due to defects in insulin action or secretion, which causes collagen to have a fixed orientation, stiffen the tissue and is likely to disrupt the normal cell interactions.

SUNBIM (Supramolecular and sUbmolecular Nano- and Biomaterials X-ray IMaging) is a computer suite of integrated programs which, through a user-friendly graphical interface, is able to perform a number of functions for (GI)SAXS-(GI)WAXS data analysis [1] such as: centering, q-scale calibration, two-dimensional to one-dimensional folding of small- and wide-angle X-ray scattering (SAXS/WAXS) data, also in grazing-incidence (GISAXS/GIWAXS); indexing of two-dimensional GISAXS frames and extraction of one-dimensional GISAXS profiles along specific cuts; quantitative scanning microscopy in absorption and SAXS contrast. SUNBIM consists of five main programs: (1) Calibration package, a set of functions allow one to find all of the geometrical parameters needed to extract a one-dimensional profile out of a two-dimensional image; (2) Batch Script & 2D Mesh Composite, to prepare batch script files (ASCII files) to run a sequential acquisition of two-dimensional frames (in scanning mode) and to perform a composite of the as-collected two-dimensional SAXS frames into a single image; (3) Single-scan (GI)SAXS and (GI)WAXS data analysis, to calibrate and fold the two-dimensional data, in order to extract relevant information from the experimental data and to fold 2D data into 1D profiles; (4) Multi-scan SAXS and WAXS data analysis, to fold each two-dimensional frame of the mesh into a one-dimensional profile and extract scattering features of the sample with a multi-modal imaging approach; (5) One-D Data Analysis Manager, a package that in addition to basic operations on one dimensional profiles (such as change of the plot representation from pixels to q, change from linear scale to logarithmic scale of the axes, choice of colors and plot thickness, inserting the legend, etc. as well as import, trigger, save and export plots) gives the possibility to denoise the folded profile and/or to deconvolute the primary beam angular divergence from the SAXS/WAXS profiles, particularly useful for a complete data analysis. SUNBIM combines in the same package both originally developed algorithms (i.e denoising, beam centering etc.) and reliable methods documented in the literature (multi-modal imaging [2], GIXAXS three-dimensional frame indexing [3]). New tools have been developed to enrich SUNBIM suite. The main novelty is the possibility to perform a deeper data reduction including dark current subtraction, background evaluation and subtraction, normalization of the SAXS intensity against the local sample thickness derived from absorption contrast maps. The advances of the new release with respect to previous one include also an automatic background subtraction from the 1D profile of the azimuthal integration to enhance peak visibility at large scattering angles (WAXS), to correct geometric aberration for small sample-to-detector distance. The previous release of the software has already been used successfully to analyse several nano-structured samples [4][5][6]. We are confident that the new features will allow a more correct and extensive analysis of the (GI)SAXS/(GI)WAXS data. SUNBIM is developed in the MATLAB language and it is distributed free of charge to the academic user (downloadable after a valid registration from http://www.ba.ic.cnr.it/softwareic/sunbimweb/)