The Alignment Menu

This menu is inactive in display_only mode. It has the following entries:

Read Alignment File

will make the microscope control program read the current alignment file.

Edit Alignment

will pop up a window (see Fig. 5.12) which allows you to insert stages and detectors, record certain devices aligned etc. Chap. 2 will tell you which one to use in which situation.

Figure 5.12: Edit Alignment window.

• Insert/Remove
  • Detector: Insert VLM: Moves the Visible Light Microscope into its inserted position.
  • Detector: Insert COUNTER: Moves the counter 2mm downstream of its inserted position.
  • Detector: Insert SIDET: Moves the segmented silicon detector 2mm downstream of its inserted position.
  • Detector: Retract Detector: Moves the detector stage all the way downstream.
  • Detector: Remove Detector: Moves the detector stage to its removed position (usually downstream/outboard).
  • Insert Laser: Moves the laser to its inserted position.
  • Insert Photodiode: Moves the photodiode to its inserted position.
  • Insert Specimen: Moves the specimen ZSTG into focus position at the current energy. Also moves ZOSA and ZDET (if detector is inserted) to their ideal positions.
  • Retract Specimen: Moves the specimen to its retracted position (usually 2mm downstream of the focus position). Also retracts the detector stage. This is for safely exchanging specimens.
  • Insert Specimen Stage: Moves the specimen stage to its retracted position (2mm downstream of the focus position). This is typically used, if the specimen stage had been removed first, or if motors have been homed.
  • Remove Specimen Stage: Moves the specimen stage to its removed position (usually downstream/outboard). Since there is not enough space for the specimen stage to pass by the detector stage in its downstream position, the VLM is moved in first, and the specimen and detector stage are moved step by step, until removed. This is typically used, to insert or remove optics (ZP or OSA).
• Record Specimen
  • Record Specimen in VLM Focus: Hit this button, when the newly inserted sample is in VLM focus. This will allow you to move the sample within about 100$\mu$m of its focus position, when inserting it.
  • Record Specimen in X-ray Focus: Hit this button, when the specimen is in X-ray focus. Based on this position, the new focus positions at different energies are calculated.
• Record Advanced Only use this menu, if you really know, what you are doing!
  • Record ZP in VLM focus: After aligning the ZP click this button, when the VLM is focused onto the ZP.

  • Record OSA in VLM focus: After aligning the OSA click this button, when the VLM is focus onto the OSA.

  • Record Detector Aligned: COUNTER: Click this button to use the current detector positions as the aligned positions for the counter.

  • Record Detector Aligned: SIDET: Click this button to use the current detector positions as the aligned positions for the segmented silicon detector.

  • Record Detector Aligned: SIDET: Click this button to use the current detector positions as the aligned positions for the segmented silicon detector.

  • Drift: Set Current as Image1: Sets the currently open image as image #1 for calculating the drift parameters (see 12.3).

  • Drift: Set Current as Image2: Sets the currently open image as image #2 for calculating the drift parameters (see 12.3).

  • Drift: Calculate Parameters: Calculates the new drift parameters from the two previously set images (see 12.3).

  • Drift: Record Parameters: Click this button, to use the entered or calculated parameters (in the fields below) as the new drift parameters. This is to activate software correction for misalignment of the microscope Z-Axis with respect to the X-ray beam axis (see Sec 12.3). Recording 0.0 for both parameters will disable drift correction.

  • You can enter the drift parameters (dx_over_dz dy_over_dz) by hand, if you want.

  • By checking one of the boxes Sobel or Roberts you can use one of the algorithms for edge enhancement, before calculating the drift in the two images. This may produce slightly different results. Experiment will show, which of them is the best one to use.

  • Sidet Z-Matching Parameter: This parameter describes the Z alignment of the silicon detector. It is defined as the ratio of the beam cone on the detector chip to the diameter of the chip's quadrant segments. A value of 1.0 therefore means that the beam cone exactly fills the quadrant segments, this is "standard". The value has to be entered by hand when the detector is aligned. The value is transferred to the server (to be written to the data files) as soon as you enter it into the field and press Enter or move the keyboard focus out of the field. The value is important for quantitative reconstruction of phase.

Align and Focus Sample with VLM

This button will pop up a window to move the three motors which are being used to pre-align and focus the sample with the VLM: The X and Y sample stepper stage and the Z detector stage (see Fig. 5.13). You could also do that with the stage and detector motor-move windows described in Sec. 5.13, but here the required motors are conveniently combined in one window, without the danger of accidentally moving the VLM for X and Y alignment or the sample for focusing.

Figure 5.13: The popup window to align and focus the sample with the VLM

Write Alignment File

will save all current alignment parameters to the alignment file.