Calculate Score Sectors

Represents the total number of identified spots within the selected ROIs. This function allows the user to calculate the percentage of spots located in a given area, such as the maze arms. The number and area of the ROIs are defined by the user, as long as at least one ROI is selected.

Results Table Output

Exporting data from imageJ's result tables to the default CSV option can led to problems related to decimal case separators. If you found this error, we recommend the usage of Excel Functions, a plugin that allows trouble-free data exports to xlsx format.

Interface

XML File

Two possible files can be used here:

1. Trackmate's whole save file
   • Ideal option overall.
   • Mandatory if you only have spots and no tracks. In this case, spots will be considered as-is, without fixing missing spots.
   • If there are any tracks, all spots outside them will get filtered out.
2. Output of trackmate's Export tracks to XML file export action.
   • Only spots in tracks get saved in this file, so only them will be considered.

Source Video

The source video used for tracking. Ideally not the processed one, so you can set the ROIs better.

Fix Missing Spots

When tracking with Trackmate, not all frames in a video will have spots. That's because your target might not be visible in those frames. It's usually not moving as well. An uneven number of frames will create an unreliable score overall. This option fixes the missing spots by using an available adjacent spot and copying its coordinates.

There's no prejudice in setting this to True if you have a perfect tracking, with spots in all frames.

If you have only spots and no tracks, this feature won't work in this mode. It is not significant to mean out the positions of scores on each frame.

Display Plots

• Pie Chart: Simple chart to represent spot prevalence in different areas by percentage.