The tracking view is where you will spend most of your time. It provides means for inspecting cells and autotracklets as well as modifying tracklets.

Hovered/Selected cell Many of TraCurate’s functions require the user to select cells. The tracking view contains general information (A) about the cell that is currently selected and the cell that the mouse pointer hovers over.

Navigation To navigate through the movie you can either click the navigation buttons (C) on the right side, use the frame slider at the bottom, or use a number of shortcuts:

Create a new tracklet Click at the cell you want to track. After clicking, you have to press the space key to set an unused trackletID. You can now navigate through the movie by pressing “d” and follow the suggested autotracklet that is coloured in … . To confirm the autotracklet, navigate to its end, hover the mouse pointer over it and press the space bar. To ensure a correct assignment, you can either look into the information table on the right side (A), or press “s” to go back and see the trackletID right over the cell. If the autotracklet contains a wrong assignment, go to the last frame that is correct, hover the pointer over it and confirm with the space bar. Then go to the next frame, hover the pointer over the correct cell and press the space bar. This now leads to the assignment of a new autotracklet you can follow further.

Alternatively to nativating through the movie with the shortcuts, you have the following strategies (E):

If there are clustering cells or other opaque situations, it is easier to track manually with the space key. Please consider, that there is a possibility to hide the object outlines (Cmd+d) to have a better view on what is going on. Sometimes also the prior movement direction of a cell is very useful in case of determining the same cell over time.

1. Remove parts of the tracklet (D): Cell tracklets can be partially removed if they were assigned wrongly. There are three possibilities: (i) only a cell object at a single time point is removed (“delete cell”); (ii) all cell objects before the current one are removed (“delete all until here”) or (iii) all cell objects starting from the current one are removed (“delete all from here”).

2. Cell division (D): If a cell divides into two, (i) track this mother cell until the last time point before division and press the space key. (ii) Now keep the mother cell selected and activate the button “add daughters”. Press “d” to see the daughter cells in the next frame and click on them. New tracklets for the daughter cells will automatically be generated if they don’t exist already. If you wrongly assigned a daughter tracklet, simply click on it again. When finished, unclick the “add daughters” button. Continue with tracking the daughter cells after selecting them.

3. Select status (B): The default state is “open”. Once you finished a tracklet, change the status to “dead”, “lost” (if a cell moves out of the image and does not come back or if cells cannot be distinguished) or “end of movie” (this status is assigned automatically to each tracklet reaching the end of the movie). The tracklet status “cell division” is assigned automatically to the mother cell, if daughter cells are added.