Cell tracking

This tool enables you to quickly step through a time series of images recorded with the observe workflow in order to track the movement of cells and re-localize them in a subsequent extraction.

Prerequisites

Only images that are recorded using the observe workflow on positions previously used for an extraction are shown by this tool.

Background information

Points, subjects and point groups

At the beginning of the extraction step of the extraction workflow, the software uses the position selected for extraction and combines it with the Point name to create a named point. This point is associated with the results (images and force curve) of the extraction and is later used to determine at which location each result was recorded. When the same cell is biopsied again, the position usually has to be adjusted to the cell’s new location. Updating the point’s position would affect the results from the first extraction, so instead, a new point is created for the new location. In order to relate the same cell to both points (with their respective position), the software associates the points with a subject using the Previous target parameter of the extraction step:

• if unset (none), a new subject is created
• otherwise, the subject selected in the list is re-used.

In this way, a series of points is related to the same subject, representing the locations of the same subject at different times.

Naming recommendations

As the observe workflow supports easy selection of a whole point group, it is recommended that the same group name is chosen during the extraction for all consecutively biopsied cells.

When performing a subsequent round of extractions following re-localization of cells, a new group name should be chosen, such that this new group contains only points of the new extractions:

For an observation following this second extraction, the new point group can then be selected to ensure that only the updated locations of the cells are observed. The same subject will afterwards show up in the cell tracking tool below both the original group and the new group, with the new group only listing observations from the second round.

Tool Overview

Cell tracking dialog with observations visible for a selected cell

Selecting subjects

Selecting a point group at the top of the dialog causes the list on the left side to be populated with all subjects that are associated with any point in the point group. Clicking on a subject expands the observations related to this subject, sorted chronologically and grouped by the point that was used for the observation.

The name of the subject can be changed using the button.

To move to the next or previous observations use the left/right arrows above the list of subjects or the ← and → keys on the keyboard.

Tracking a cell

To mark the location of the cell simply left-click on it in the image view, this will also add a next to the timestamp of the observation.

When moving to the next observation image, the locations of the cell in all previous observations is outlined in blue:

To remove the mark, right-click on it. If you want to change the position instead, left-click on the image at a different position.

When you are finished tracking the cell, or if you want to save intermediate locations of the cells, be sure to press the Save Changes button before closing the dialog, otherwise the locations will be discarded.

Adjusting the image

Zoom in/out

Scroll with the mouse wheel while holding down the Ctrl key.

Move around

Press the left mouse button while holding down the Ctrl key, then move the mouse around (keeping the mouse button pressed).

Change transparency of the cell’s outlined path

Use the slider in the upper right corner or scroll with the mouse wheel while holding down the Shift key.

Annotating an observation

The annotations bar below the image allows you to annotate each observation image with expressions (or “tags”) of your choice. For example, you could annotate images where a cell detached from the surface with “detached”. To add an annotation, click in the text box, enter your expression and confirm with the Return key. Alternatively, the software offers a drop-down list of all the existing annotations it finds for the active experiment.

After adding or removing an annotation, be sure to press the Save changes button.