The 3-dimensional Dataset

Any scanning microscope works by scanning the sample through a probe (or vice versa), where the probe is a focused x-ray beam in our case. One nice feature of a scanning instrument as compared to a full-field microscope is that you can record multiple signals ("detectors" or "data channels") for each scan pixel.

In the case of Outboard STXM, these channels can be the total transmitted intensity (recorded by the proportional counter as number of photons) and the clock signal, which records how long the x-ray beam dwelled on each scan pixel (by counting pulses from a fixed-frequency clock). Outboard STXM also has analog (voltage) inputs, but they are not used in standard operation.

In the case of Inboard STXM, the standard detector is a silicon detector with eight segments. Therefore, we usually read eight signals per scan pixel, plus optionally the clock signal. The silicon detector puts out a voltage which can be converted to photon count rate by application of a calibration formula (see Chap. 10.7).^9.1

Therefore, we always end up with a 3-dimensional array of data, where the first two dimensions are the X and Y image (scan) dimensions, and the third dimension holds the various signals recorded for each scan pixel (see Fig. 9.1). The size of the 3rd dimension can also be one in certain cases.

Figure 9.1: The 3-dimensional STXM 5 dataset. Dimensions 1 and 2 are the X and Y image pixels, whereas the 3rd dimension holds all the signals (detectors) which are recorded for each scan pixel. In this particular case, all eight silicon detector (Sidet) segments plus the clock signal were recorded.