Larvae Tracking

Pre-process the input video to make it suitable for Trackmate analysis. These steps include frames duplication and inversion, as Trackmate algorithm recognizes white spots in a dark background. Background subtraction trough average subtraction is also performed.

A TrackMate tutorial can be found here.

FPS reduction

We found 20 fps to be suitable to track larvae fish movement. It's possible to change the framerate using this plugin's FFmpeg tool

Interface

Input Video

Any videos supported by ffmpeg. This includes most video formats in existence. Notably, one exclusion: AVI videos saved from ImageJ with compression set to "None" (codec rawvideo) will not work.

Output File

The path to save the operation's output.

Output Formats

The user can choose between AVI, TIFF or MP4.

Start and End frame

Specify the frame number to begin and end the processing.

The selection is inclusive, meaning both the start and end frames will be processed.

Frame numbers are one-indexed (the first frame has a frame number equal to 1).

To process the video all the way to its final frame, enter 0 in the 'End frame' field.

Preview

Shows a preview of the function, using the first 10 frames ahead of the Start frame set by the user.