Method 1: Calculating the shift

1. GTS Rotation 0°

2. Draw annotation circle same size as sample/feature of interest.

3. Configure to be at Y 1280 and X 1080.

4. Move sample/feature using X step to recover it in the centre of circle.

5. GTS Rotation 90

6. Move sample/feature using Z step to recover it in the centre of the circle.

7. Check positions at 180 and 270 and with full rotation (0-360) to ensure feature remains centered.

Method 2: Circle method (Easier, slightly less precise)

1. GTS Rotation 0°

2. Draw annotation circle same size as sample/feature of interest.

3. Configure to be at Y 1280 and X 1080.

4. Move sample/feature using X step to recover it in the centre of circle.

5. GTS Rotation 90

6. Move sample/feature using Z step to recover it in the centre of the circle.

7. Check positions at 180 and 270 and with full rotation (0-360) to ensure feature remains centred.

For Samples larger than the FOV:

1. Mount sample on GTS

2. Set GTS Rotation to 0 degrees

3. Use GTS X to move the specimen until one side aligns with the edge of the FOV.

4. Record the GTS X position

5. Use GTS X to move the sample in the opposite direction until the other edge aligns with the FOV.

6. Record the 2nd GTS X Position.

7. Calculate the centre of these two points and enter the value into GTS X.

8. Set GTS Rotation to 90 degrees.

9. Repeat steps 3 to 7 using GTS Z motion.

10. Once sample is centred along X and Z axis the sample will be on the COR.

• Notebook for calculating X,Y Theta coordinates from pixel X,Y in reconstruction