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

Figure 6 XANES stack of images to extract raw spectra Calcium map Notes: XANES raw spectra (require postprocessing) 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 raw spectra data, 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. Calcium (Ca) maps can be generated by subtracting a pre-edge frame (from the first frames of the stack) from a frame corresponding to the maximum Ca absorbance.