Contents

• setup_microscope

setup_microscope

This module consists of methods which configure microscope hardware based on reference files.

microscope_automation.hardware.setup_microscope.setup_cameras(specs, microscope)

Setup cameras and add to microscope object

Input:

specs: hardware specifications which info on cameras will be retrieved from

microscope: microscope object which cameras will be added to

Output:

none

microscope_automation.hardware.setup_microscope.setup_pump(specs, microscope)

Setup autofocus and add to microscope object

Input:

specs: hardware specifications which info on autofocus will be retrieved from

microscope: microscope object which autofocus will be added to

obj_changer: objective changer object to attach to this autofocus (Defult: None)

Output:

none

microscope_automation.hardware.setup_microscope.setup_stages(specs, microscope)

Setup stages and add to microscope object

Input:

specs: hardware specifications which info on stages will be retrieved from

microscope: microscope object which stages will be added to

Output:

none

microscope_automation.hardware.setup_microscope.setup_autofocus(specs, microscope, obj_changer=None)

Setup autofocus and add to microscope object

Input:

specs: hardware specifications which info on autofocus will be retrieved from

microscope: microscope object which autofocus will be added to

obj_changer: objective changer object to attach to this autofocus (Defult: None)

Output:

none

microscope_automation.hardware.setup_microscope.setup_focus_drive(specs, microscope, obj_changer_id=None)

Setup focus drive and add to microscope object

Input:

specs: hardware specifications which info on focus drive will be retrieved from

microscope: microscope object which focus drive will be added to

Output:

none

microscope_automation.hardware.setup_microscope.setup_obj_changer(specs, microscope)

Setup objective changer and add to microscope object

Input:

specs: hardware specification from which info on objective changer is retrieved

microscope: microscope object which objective changer will be added to

Output:

objective_changer_object: instance of ObjectiveChanger which was just added to microscope

microscope_automation.hardware.setup_microscope.setup_safe_areas(specs, microscope)

Setup safe area to prevent crashes between stage and objective. Adds safe areas to microscope object

Input:

specs: hardware specifications which info on safe areas will be retrieved from

microscope: microscope object which safe areas will be added to

Output:

none

microscope_automation.hardware.setup_microscope.setup_microscope(prefs)

Create object of class Microscope from module hardware.

Input:

prefs: preferences with information about microscope hardware

Output:

microscope: object of class Microscope