Microstage¶
Description¶
The microstage is responsible for the general positioning of the assay inside the flowcell. It accomplishes this not by moving the assay itself, but by moving the flowcell around the assay.
What is what in the user interface¶
The microstage UI is composed of these parts:
flowcell viewer
toolbar
flowcell selection
waypoints list
path selection
steps list
Usage¶
Position and moving¶
All the positions in the microstage are relative to the flowcell.
The values are measured in millimeters (mm) and increase in the top-down and left-right directions.
The speeds are measured in millimeters per second (mm/s).
Microstage position indicator¶
The square drawn in a solid blue line in the flowcell viewer indicates the current position of the Brightfield camera’s field of view (FOV). This is the main area where assays are performed. Since controlling this position is the main function of the microstage it is commonly known as the microstage position.
Microstage limits¶
The big square drawn in a dashed blue line represents the microstage movement range. Moving outside these limits is dangerous and the system will not allow you to do so. If the system detects the current position is outside this safe range, any movement will be automatically redirected to inside the limits.
Position readout and axis locking¶
The position readout can be viewed in the toolbar, and by clicking on it, the wanted axis can be locked for specific actions. When an axis is locked, the affected actions won’t move the microstage along it.
In general, it can be said that the axis lock only affects actions that don’t explicitly define their target position.
Axis lock affects:
The stepper keypad.
The joystick.
Axis lock does NOT affect:
Clicking on waypoints – each one defines a target position.
Moving along the path steps – each one refers to a waypoint, which has a target position.
Python scripting – the target is part of the API:
microstage.move_to(x=..., y=..., ...)ormicrostage.move_by(dx=..., dy=..., ...).
Movement speed¶
The speed can be viewed and configured in the toolbar. By default, the speed bar shows the approximate speed of the device. The microstage movement speed can be locked by clicking the speed button and selecting the desired speed in the slider or spinbox.
In general, it can be said that the speed lock only affects elements that do not define their own speed.
Speed lock affects:
Clicking on waypoints.
The stepper keypad.
The joystick.
Speed lock does NOT affect:
Moving along the path steps – each one defines its own approach speed.
Python scripting – speed is part of the API:
microstage.move_to(..., speed=...).
Moving using keypad¶
You can move the microstage in steps by using the keypad found in the toolbar. You can select the size of the step in the spinbox.
Moving using the joystick¶
By default, you can control the microstage by moving the joystick while holding down the trigger button. When holding the trigger button, the flowcell viewer will be highlighted with a blue border to indicate that the joystick will now move the microstage. The joystick movement speed depends on how much you move the stick; fully deflecting it will move the microstage at its maximum speed while small movements will move the device slowly.
Waypoints¶
Waypoints are named positions in your flowcell. They are the easiest way to move to predefined points in your experiment. The existing waypoints can be seen in the waypoints list and the flowcell viewer. Clicking a waypoint icon will move the microstage to that position.
Waypoints list¶
You can see all your waypoints in the waypoint list. For convenience, you can freely reorder the waypoints by dragging and dropping them. You can also select waypoints by clicking them. You can edit the name and position of a waypoint by double-clicking it. (Note: You need to hit enter to confirm the change).
On the lower part of the list, you can find a few tools to manipulate your waypoints. From left to right in the UI:
The “store position” button updates the position of the selected waypoint to the current position of the microstage.
The “add to path” button adds a selected waypoint to the current path.
The “duplicate” button duplicates the selected waypoint.
The “add” button creates a new waypoint using the current position of the microstage.
The “trash” button deletes the selected waypoint.
Paths¶
Paths are user-defined series of waypoints that can be visited in a more automated way. They are composed of steps that can be edited and viewed in the steps list. You can configure multiple paths and change between them at any time.
The path can be viewed as green line connections between the waypoint in the flowcell viewer.
Steps list¶
The steps list shows a detailed view of your current selected path. The steps are numbered from top to bottom. The current step is marked with a blue square around its number while the destination step is marked with a white square.
You can reorder the steps by dragging them. You can see a step’s details by clicking its “down arrow” button. Here you can also choose an “approach speed” and a “dwell time”. The default speed is zero, and in this context means that the device will move at maximum speed. When expanded you can also see the “trash” button where you can delete the step.
Moving along the steps¶
On the lower part of the list, you can find the controls to move along the steps.
The “first” and “last” buttons will move directly to the first and last step in the list respectively.
The “previous” and “next” buttons will move to the previous and next step in the list respectively.
The “play” button will move through all steps in order until stopped.
The “stop” button will immediately stop any movement of the microstage.
Selecting the flowcell model¶
To show the correct diagram of your flowcell, select its model in the combo box. You can also reload the default set of waypoints by selecting “Load default waypoints” in the drop-down menu.
Warning
Reloading the waypoints will clear all the paths for this session.
Adjusting the flowcell position¶
As described before, the positions in the microstage use the flowcell as a reference. This means that after changing or repositioning the flowcell in the instrument, the UI may not reflect the actual position in the flowcell. To fix this we can adjust UI to match the real flowcell. To do so, navigate across the flowcell while looking at the Brightfield camera until you observe a recognizable position, such as a corner, on the real flowcell. With the edge of this corner in the middle of your camera, right-click that position in the flowcell UI and select “reset flowcell position to here”. Then right-click that position in the flowcell UI and select “reset flowcell position to here”.
Troubleshooting¶
Issue¶
The position shown in the flowcell viewer does not correspond to what I can see on the camera.
Possible solution¶
First, you need to see the flowcell in the brightfield camera. If you cannot, check if the correct camera is selected and try adjusting its settings. Finally, you can adjust the flowcell viewer to match the camera view by following the procedure described in the Adjusting the flowcell position section.