Tracker

Tools > Tracker > Settings, and Tools > Tracker > Show Traces to draw the tracks.

Linking joins the detections of one cell in successive frames into a track.

Settings

• Method: see the table below.
• Search range: how far a cell may move from one frame to the next, in pixels (a length; with a calibration also shown in µm per frame). Too small breaks tracks, too large joins neighbours.
• Memory: for how many frames a cell may go undetected and still keep its track.
• Buffer frames: frames at the start that only train the background and are not tracked.
• Trace length and thickness: how the tracks are drawn.

Method	What it does
Nearest position	Each cell is linked to the nearest detection in the next frame, for all cells at once (Crocker and Grier)
Nearest predicted position	The same, searching around where the cell's last step says it will be. Better in fast flow
Flow assignment	Written for flow in one direction along the picture's horizontal axis; links against the flow are not made
Flow assignment with gap closing	The same, plus a second pass that joins track pieces across longer gaps

The folder button loads a linking method from a Python file.

Tracking a recorded video

Set the frame range in the Chopper (the two marks on the slider show it), then press Track. The status bar shows the progress; Esc stops and keeps the frames tracked so far.

Cell IDs can differ between two runs of the same video; the tracks are the same.