Synchrotron cryo-soft X-ray microscopy sheds light on the interaction of bacteria with nanostructured calcium phosphate substrates

Figure 7 & S3 XANES stack of images around the L3,2 edges to extract raw spectra data. Calcim maps Notes: XANES raw spectra data can be extracted by opening the XANES datasets in FIJI, selecting the desired region of interest (ROI), and using: Image → Stacks → Plot Z-axis Profile. In some spectra, isolated abnormally strong peaks may be observed at single wavelengths. Values at wavelengths exhibiting such isolated peaks should be removed to obtain a smoother and more representative spectrum. To obtain comparable XANES spectra for bacteria incubated on the small topography, the spectras must be reduced matching the background noise level observed in the other experimental conditions. Compare the average of pre-edge values of small topography spectra to the average value in the other condition to get the reduction factor (resulting in 10 fold reduction approx).