Well scan

This workflow moves the system around in the area of a well in a way that allows you to view and inspect the whole area piece by piece without gaps in between.

Parameters

Parameter Description
Scan area option Determines which portion of the wells’ areas are to be scanned (see Full well area and Reachable area)
Reduce the area to scan Allows to reduce the size of the scanned area (e.g. only 90% of a full well’s diameter)
Scanning direction Determines where the scan is started and how it progresses through each well
Save images Optionally save an image at each position to a given folder

Full well area

Scan the full area of the well. This is only available when the corresponding plate is in observation mode.

Because there is some slackness when placing the plate and positioning cannot be guaranteed to be 100% accurate, it is necessary to calibrate the position of each scanned well. The system will guide you to the calculated calibration position and you will have to center the corresponding feature of the well to the center of the screen:

In case of circular wells this is the center (in X) of the top arc:

calibration point circle

For rectangular wells this is the top left corner.

calibration point rectangle

Reachable area

Scan only the area of the well which is reachable by the tip. This is also possible when the plate is not in observation mode.

In this case it is possible to configure the Z position of the cantilever during scanning:

Cantilever position option Description
Observation height Keeps the probe above the plate at the configured observation height.
Content height Lowers the probe to the content height (only if the plate is not in observation mode, otherwise it will be kept at observation height)

Note

When Content height is selected, the effectively scanned area may not correspond to the complete reachable area, because the workflow only generates uniformly distributed positions around the well’s center and will only access points that are within the reachable area: covered area

Scanning

After starting the workflow you may have to calibrate the exact position of each selected well as described above and adjust image focus as well as imaging settings.

When the scan of the a well has started use the Previous and Next buttons or the left and right arrow keys on the keyboard to move forward or backward to the next position.

Hint

It is possible to use dragging movements in the video view after each move. When continuing after this, the system will move to the next (or previous) position as if no dragging had occurred.

To make the system continuously move to the next or previous position select the Automatically move to next/previous option and then navigate either forward or backward. The system will then keep moving in the chosen direction at a slower speed until it reaches the end of the current well’s scanning area or Automatically move to next/previous is deselected (it will still perform one final move to the next position after this).