Rework Step Class

[Formanj-0]

This will be complicated and require some thought.

The step class currently has a run method that compiles all the params into kwargs, then runs them through main. I would like to move the parameters that do not changes during the running of the step to the init of each step to make them clearly defined.

I would also like to break up main into a iteration part and a run one image part. The iteration part should be a part of main, and the run one image should be its own method. This will allow for easier debugging and easier connection to the microscope.

Do not rush this issue cause it will take some effort into getting everything in place.

[Formanj-0]

This will also help with parallelization of none prePipeline steps