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Well scan workflow

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Maria Milla

The Well scan workflow allows you to scan the well area piece by piece without gaps in between and can be used to find a single cell in the cell culture well.

After opening the workflow, it displays the plate layouts indicated in the software. Use the Exchange Plates workflow to change the plates and set the system to Observation mode. You can choose the wells for investigation by clicking on them. The selected wells will turn blue.


Well scan workflow

The scan area option determines which part of the well can be scanned, because the available area depends on the cantilever position. The “Reachable area” corresponds to the area in the well that is reachable with the tip. While keeping the cantilever in the observation height, the effective scanning area is larger compared to the reachable positions at content height. If the cantilever position is on the observation height, it is kept above the plate at the configured observation height (shown in the Exchange Plate workflow), and thus, not immersed in liquid. If the cantilever is on the content height, the cantilever is lowered to the content height (shown as well in the Exchange Plate workflow), and immersed in liquid. As previously indicated, it is important to note that 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:


The explanation of the scannable areas within the well depending on the cantilever position

Keep in mind that the cantilever in observation height is not immersed to liquid, so the protective droplet around the cantilever can dry out after being in air for about 10 minutes and the probe may become unusable (especially when it was previously in contact with buffer solutions or cell culture medium).

“Full well area” corresponds to, as the name indicates, the full area of the well. If you choose “Full well area” under Scan area options, the plates must be set to Observation mode (using the Exchange Plates workflow), otherwise it is not possible to use the workflow.


Full well scan is not possible when plates are not set to observation mode

Following the next steps in the workflow, you can modify the size of the scannable area. By reducing this percentage, the scanning area and, thus, the scanning time are reduced.

Image order refers to the position, where the imaging starts. When choosing “Meander from top left”, the scanning starts from the top left of the imaging area. When choosing “Spiral outwards”, the imaging starts from the center of the chosen well and moves in spiral steps towards outside. Optionally, the images can also be saved after selecting the folder.

When you choose to save the images, folder selection appears and destination folder can be chosen

After pressing “OK” on the workflow, the position in each well before the scanning must be calibrated. The calibration position depends on the shape of the well. For circular wells, the calibration position is the center of the top arc:

Calibrating the well before starting the scan

After the calibration, the well scan workflow starts by going to the chosen well. For inspecting the well, you can manually press Previous/Next buttons or left and right arrow keys. This will move the stage in the selected well frame by frame. When enabling “Automatically move to next/previous”, the workflow moves automatically frame by frame in the selected well. For activation, press “Next”. In case several wells were selected, you can travel to the next well by pressing “Next well”. “Abort” will stop the workflow. When reaching the last selected well, “Finish” stops the workflow.