The Fiji distribution of ImageJ comes with several manual tracking tools, two of which are particularly useful:
- Plugins->Tracking->Manual Tracking
- Plugins->Tracking->Manual tracking with TrackMate (TrackMate is an advanced automatic tracking tool, with the option for manual editing of tracks)
The Manual Tracking plugin is quick to use, intuitive and produces easy-to-understand output. TrackMate has the advantage that automatic detection and linkage can be combined with manual input.
MtrackJ (**see the component page here) can be installed via Fiji update sites. It has many shortcut keys enabled so for manually tracking many data, it will become quite efficient as you get used to the short-cut key operation.
Pre-processing steps before manual tracking might include:
- denoising and/or deconvolution
- flicker and photobleaching correction, e.g. using Fiji's Image->Adjust->Bleach Correction
- flat-field correction, and/or bandpass (ImageJ's Process->FFT->Bandpass filter) according to the size of the features of interest