Hardware configuration

A crucial issue is that different rigs can have different pieces of hardware, mounted in different configurations. For example:

• Different controllers and manipulators (Luigs, Sutter, Scientifica etc)
• Two manipulators outside the XY stage.
• Two manipulators on the stage
• Two manipulators on the stage, and an additional motorized chamber independent of stage
• Several microscope objectives

We want to automate hardware configuration as much as possible:

1. Recognize controllers.
2. Recognize configuration.
3. Assign manipulators to motor channels.

A simple start would be that we display motor coordinates for all channels, and the user assigns them manually to the different manipulators. Recognizing controller might be doable by trial and error. Recognizing configuration can be automated, as we will look for general affine transforms from (XYZ manipulator, XY stages) -> (XY screen, focal Z).

Automation of channel assignment

Different ideas:

1. The user moves along one axis with the hardware controller, and the program finds out the channel.
2. The programs moves one (unknown) axis, and the user reports on which axis is being moved.
3. The user mounts a pipette and puts it in focus. The program tries all axes and checks on screen what is being moved. However there must be a background (coverslip) to avoid confusions.

Both (1) and (3) requires to have a physical hardware controller. Thus (2) is probably best.

This would be done in a separate program for hardware configuration.