PI stage setup
If you are using PI stages, you should ideally optimize their motions using PI MikroMove. The following is a list of things to do, but without detailed instructions.
First of all take a record of the factory settings of your stages. Right-click on each axis, select "Show Exapanded Single-Axis Window"
Load the stage with the water bath and fire up the data recorder for each axis: click the axis name in the menu and select "Show data recorder". Make steps of the sizes you typically use during tile scanning. Look at the curves. They should settle in under about 150 ms with a target velocity of 25 mm/s. A V-551-2B stage can settle in under 100 ms. A faster velocity does not help because the stages will not achieve it over such a short distance. You will need to adjust the number of recorded data points or sampling rate (bottom left) to see the whole curve. If the stage position poorly follows the command position then you can try tuning the PID loops (see below). If the command position is changing too quickly, try increasing the speed and acceleration.
Ensure that the stages are also able to perform large motions (20 or 30 mm).
You can confirm all is good by imaging pollen grains and moving the stages.
Note that with larger step sizes and faster speeds the water in the bath can cause image to oscilate for a short while. If this is problematic: decelerate more gradually, use slower speeds, reduce the water bath volume.
Once all steps are complete and the microscope is assembled, you can set the soft limits (min and max positions) for the X and Y axes so that even at the firmware level, stages can't accept out of bounds motion commands that would cause hardware damage. BakingTray has its own soft-limits, though, so this step is optional.
Tuning the PID loops
The direct-drive stages have separate loops for position and velocity.
Other stages have multiple loops for other purposes. If your tuning changes do nothing, try a different loop.
Enable the display of the startup parameters. This will make going back to the original values easier.
Set the I and D terms to zero. Set P to a low number (e.g. 10). Perform a step of the size and speed typical of tile scanning.
Keep doubling P until you see oscillations, then halve it.
Set I to a small number (e.g. 5) and keep doubling it as long as the curve improves. Look for where it settles to a steady state and has reached the target position. Keep going until it oscillates then halve it. If the curve looks good earlier then you don't need to push that far.
Tweak D if needed, but otherwise leave at zero.
Once well tuned a V-551 stage can make a 1.25 mm stage in about 100 ms whilst loaded with a water bath:
Hints and tips
Ensure that the stage really is settling as expected. e.g. If you are are planning on moving in 1 mm steps and settling well within, say, 200 ms then make sure that you can successfully issue 1 mm motion steps every 200 ms. Ensure that every so often the stages aren't taking much longer to settle. This can happen and it will really slow down your acquisitions. Tweak PID parameters until this no longer a problem.
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