Basic calibrating procedures

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Theory
BakingTray performs a tile scan over the sample. The individual tiles are later assembled into a single image by StitchIt. In order to place the tiles accurately and produce a good quality stitched image you will need to ensure that the following are true.
The X and Y scanners must displace the beam along orthogonal directions. 
The X and Y stages must displace the sample along orthogonal axes. 
The X scanner should move the beam along the direction of motion of the X stage and the Y scanner along the direction of motion of the Y stage. 
The scanning plane (imaging plane) should be parallel with the plane of motion of the X and Y stages.
The blade must be parallel to the Y stage such that the cuts it produces cause the surface of the sample to remain the same distance from the objective as it is translated in Y. 
Practice
This is what you must do to achieve the above.
Ensuring the X and Y scanners are orthogonal
Recall that the X and Y scanners must displace the beam along orthogonal directions and the beam must leave the scanhead at 90 degrees to the angle with which it entered. The alignment needs to be done once when the microscope is built.
If you have a close-coupled scanner pair you can place it on the table, feed the beam going into it parallel with the table and orthogonal to the scan head box. The scan head should be clamped to the table. Rotate the scanners in their mounts such that the beam exits the scan head parallel with the table and at right angles to the angle at which it came in. You can use the table hole pattern to guide you. Remember to set galvos to their mid-point by feeding in a zero command voltage. Now apply a sinusoidal command voltage to each axis in turn, project the beam onto the wall and ensure the two motion directions are orthogonal.
If the above alignment isn't possible (e.g. you don't want to dismantle your microscope) then you could opt to image an EM grid and check whether the grid lines are orthogonal.
If you find the scanners aren't orthogonal to each other then this can only be corrected by altering relative angle of the shafts. Depending on how the scanners are mounted this may or may not be possible. If you can't correct this, it can be done in software, later.
Ensuring the X and Y axes displace the sample along orthogonal directions
The X and Y stages should displace the sample along orthogonal axes. This can be quite hard to measure. It might be best done by imaging with a camera, where you know you are dealing with a square pixel grid. If this step is hard to measure, then skip it for now and only come back to it if you have problems with stitching images that you can't correct.
Calibrating the number of microns per pixel
At this point it is helpful to calibrate the number of microns per pixel in ScanImage and to ensure that the pixels are square.
Ensuring the scan axes are aligned with the stage axes
Recall that the X scanner should move the beam along the direction of motion of the X stage and the Y scanner along the direction of motion of the Y stage.
To achieve this, image pollen grains in ScanImage. Right-click on the image window and enable the cross-hairs. Translate a pollen grain along the cross hair of one axis. It should follow it perfectly. If not, rotate the stage assembly about its centre to achieve perfect tracking. You want to get this as accurately as possible. Within a micron if you can.
Then check the other axis. If the scanners and stages are both orthogonal, then you should also get perfect tracking along this axis. If not, as mentioned above, small differences can be corrected at stitching time by introducing a shear to the images.
Ensuring the imaging plane is parallel with the motion plane
The scanning plane (imaging plane) should be parallel with the plane of motion of the X and Y stages. You will need to mount the stages on three points of contact with at least two being height adjustable. Image a thin fluorescein layer under a coverslip. Translate the stages two or three mm. The image should not change. If it does, the slide is tilted and you need to re-mount it. Assuming the image plane is not curved, the whole FOV should snap into view at once as you focus through it. If there is field curvature you will likely see the centre appear first and as you move the objective further down you will see a donut. If the stages are aligned with the image plane, the donut should be symmetric.
Ensuring the blade is parallel with the Y axis
The blade must be parallel to the Y stage such that the surface of the sample remains the same distance from the objective as it is translated in Y. Adjust the blade angle to achieve this. This adjustment may need to be repeated periodically depending on your vibrotome. 
The above alignments should be made in the order listed above. Once done, ensure that no out of bounds motions are possible by setting the min/max position values for each axis. This is important for ensuring the hardware can't be damaged.
See also
​Setting up stages​
​Fine tuning positioning accuracy​
Calibrating a linear actuator
Calibrating image size
Last modified 2yr ago
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Contents
Theory
Practice
Ensuring the X and Y scanners are orthogonal
Ensuring the X and Y axes displace the sample along orthogonal directions
Calibrating the number of microns per pixel
Ensuring the scan axes are aligned with the stage axes
Ensuring the imaging plane is parallel with the motion plane
Ensuring the blade is parallel with the Y axis