16

SOPHIE Alignment

watts edited this page 2025-10-31 10:43:56 +01:00

Table of Contents

• General Introduction
• The SOPHIE Endstation
• Fixing the SOPHIE Alignment
• Characterise the Virtual Drift
• Fix the Virtual Drift
• Characterise and Fix the Real Drift (Requires X-rays)
• Apply a Software Drift Correction

General Introduction

Microscopes based on Fresnel zone plates will often suffer from "energy drift" where the position of an observed sample feature will vary linearly with respect to the photon energy. This drift is due to systematic positioning errors that occur when the zone plate Z-axis stage moves, and has two parts:

• Real Drift: The main drift problem is caused by the ZP stage not moving parallel to X-ray beam axis.
• Virtual Drift: A related indirect drift problem is caused by the interferometer mirror surface not being parallel to the ZP stage movement, and the measured change in laser path length being included in the feedback system to erroneously adjust the sample fine stage.

Note that a drift will appear worse when looking more closely at it, i.e. the more one zooms in on a sample region, the more sensitive the measurements are to the drift. One should also never expect to completely eliminate drift, but only to minimise it until it is no longer significant.

The consequences of an energy drift include:

• Misaligned data: The data stacks must be aligned image-by-image in order to correctly interpret the observations.
• Image Padding Requirements: Image stacks require padding in order to keep features of interest within the measured area over the full energy range.
• Limited Fine-stage Movement: A large virtual drift will apply a significant feedback voltage which can push the limits of the sample fine stage and cause a mismatch between the calculate scan-tile regions and the achievable fine stage regions.

There are a number of strategies for dealing with energy drift:

• Post-fix: Simply align the images during the data analysis.
• Rotate Endstation: This essentially adjusts the X-ray beam axis. One can choose to either minimise the real drift, or to match the virtual drift (with opposite sense) so that they cancel each other out. Note that translating the endstation also results in a small rotation of the X-ray beam axis and so one should take care to reoptimise the endstation position after each rotation. The size and distance of the entrance apertures may limit the amount of endstation rotation that can be applied before the beam is clipped.
• Adjust Interferometer Mirrors: This can be applied to either minimise the virtual drift, or to cancel the real drift. In practice, such adjustments can be very difficult and inconvenient due to the need to vent the system to access the manual adjustment screws and a limited number of adjustment screws included in the implementation of the interferometer system. One must also meet the constraints of having the interferometer beams sufficiently overlap at the detector.
• Software Correction: Drifts can be countered by applying a ZP-Z dependent correction to the transform to X/Y position that is calculated by Orocos. A software correction can cancel a virtual drift completely by neutralising erroneous feedback and the only negative consequence would be an extra (but typically insignificant) shift in the coordinate system when the interferometer is reset. However, using a software correction to minimise a real drift will increase feedback signals and can cause issues with the fine stage limits in extreme cases.

The SOPHIE Endstation

The SOPHIE endstation uses a novel interferometer design where:

1. The measured axes are not along the X and Y axes, but inclined by 45° (rotated about the Z-axis). The interferometer measurements are transformed into X and Y positions in software (Orocos), which will be referred to as the J and K axes.
2. The beam-splitter for the ZP stage is fixed to the ZP-Z stage and so the laser beam's contact point travels along the outer reference mirror when the ZP-Z stage moves.
3. The J/K interferometer mirrors attached to the ZP and sample stages are glued into fixed positions with no possible adjustments in order to reduce size and weight.

Figure 1. Schematic of the SOPHIE position-interferometer design. The red and blue lines are the two orthogonal linear polarisations of the laser beam and their reflections from the polarising beamsplitters (yellow) are offset to clarify the beam trajectories. The green objects are quarter-wave plates that rotate the beam polarisation by 45°. The corner cube will always reflect the beams along a trajectory parallel to the incident beam, but with a small position offset (determined by how far the incidence point is from the central corner).

Figure 2. Render of the interferometer parts in SOPHIE. The current discussion centers on the XY-position interferometers while the Z-position and angle interferometers do not affect the drift issues.

In this design the virtual drift is determined by the long reference mirrors in the upstream, lower corners of the vacuum chamber. The initial mirror alignment involved setting the reference mirror parallel to the corresponding mirror mounted on the ZP stage.

Figure 3. Design drawings and 3D render of the reference mirrors. The alignment screws (P25SB100V) have a thread of 1/4''-100 and so each full turn will change the local mirror height by 25.4 microns (clockwise to raise mirror face). Turning the 2 upper screws by a full turn in opposite directions will adjust the tilt of the mirror by 0.56 mrad.

Fixing the SOPHIE Alignment

Characterise the Virtual Drift

1. Ensure that no software drift correction is being applied by checking the values of zCorrectMatrix in the Orocos Deployer and then setting both elements to zero:

Sensor1.zCorrectMatrix[0] = 0.0
Sensor1.zCorrectMatrix[1] = 0.0

2. Open the interferometer EPICS panel (xsophie-sioc-ec1:~/StartupScripts/start_panel_ZMI) to see the raw outputs from the J/K interferometers before they are translated into X/Y positions. These values will be in terms of fringes and can be interpreted in microns by multiplying by the sensor resolution factor set in start.ops (0.0001545388). (Alternatively, turn off the transformation by setting Sensor1.transform=0 in start.ops, which will also disable the software drift correction).
3. Switch off the sample stage feedback by jogging the coarse sample stage.
4. Note the interferometer values and ZP-Z position.
5. Move the ZP-Z stage by a defined amount.
6. Note the new interferometer values and ZP-Z position.
7. Calculate the effective mirror tilts of the J and K interferometer reference mirrors.
8. Calculate the number of screw turns required to remove the calculated tilt from the reference mirrors.

Figure 4. EPICS panel for ZMI interferometer values and diagnostics. The "POS" values are the number of counted interference fringes, the "Status" values that end in a 5 indicate an OK status, and the "SSI" values are the signal strength indicator. An SSI value above 10k is good, but be sure to also check that blocking a beam causes a significant drop in SSI.

Fix the Virtual Drift

Apply the calculated screw turns to make the reference mirror parallel to the ZP stage movement. and then further adjust the interferometer components to compensate the beam alignment and optimise the signal strength.

If one is unable (or unwilling) to get the interferometer signal high enough to reliably lock after adjusting the reference mirrors, then the drift correction could instead be applied to the software zCorrectMatrix.

Characterise and Fix the Real Drift (Requires X-rays)

1. Find an easily locatable feature that is also small and doesn't change in appearance very much when changing photon energy. A metal particle close to the corner of a membrane is ideal. Symmetry is often important.
2. Select a pair of photon energies that will give a significant difference in focal length (i.e. movement of the ZP-Z stage).
3. Measure the position of the object at each energy and note the change in position.
4. Rotate the endstation using the Girder Mover.
5. Optimise the X-Y position of the Girder Mover for maximum X-ray signal.
6. Iterate steps 3-5 until the drift is minimised.

Apply a Software Drift Correction

The zCorrectMatrix values [X,Y] are applied by Orocos in the J/K->X/Y coordinate transform. This means that all of the bad effects of a virtual drift are neutralised at the Orocos level. The only negative effect would be a (typically insignificant) shift in the coordinate system when the interferometer is reset at a significantly different photon energy from the previous reset. This occurs because the correction is calculated based on a reference point that is chosen as the position of the last "reset interferometer". Since an interferometer reset also defines a new coordinate system based on a reading of the position encoders on the coarse stages (with the fine piezo stage in a relaxed, 0 mV position) (and there will also be a coordinate shift due to previous positions being incorrect via accumulated errors in counting fringes), there is typically going to be a shift in the coordinate system anyway that will be more significant than the zCorrectMatrix shift.