git clone https://github.com/yngvem/zebrafish_manual_track_gui.git
cd zebrafish_manual_track_gui
pip install -e .
python3 scripts/tracker.py
- Load ims-file containing zebrafish bloodflow video
- Wait for image loading and preprocessing (takes a while, GUI will not respond but there is a progress bar in the terminal window. There is also a wait once the progress bar is at 100%)
- Adjust contrast by right-clicking and moving mouse up/down and left/right
- Left click to mark a single particle
- Left click multiple times to adjust position of mark
- Use arrow keys on keyboard or buttons in GUI to navigate frames
- Mark the same particle in the next frame
- Repeat step 6-7 until particle dissapears (either out of bounds or out of focus plane)
- Navigate back to the particle's first frame
- Press [+] button to generate new particle track
- Repeat step 4-10 untill there are no particles left in the first frame
- Go to the next frame, and repeat step 4-11 for all unmarked particles
A YAML file with the particle track will be stored in the same folder as the data-file for every frame-change. If the image-stack file is called filename.ims, then the track-data file will be named filename-manualTrack.yml. The track-data file (if it exists) will be loaded automatically with image files.