behavior annotator with napari
The simple tool for animal behavior annotation to create a CSV file that looks like this:
frame, behavior
1, behaviorA
2, behaviorA
3, behaviorA
4, behaviorA
..., ...
98, behaviorA
99, behaviorA
100, behaviorB
101, behaviorB
102, behaviorB
..., ...
pip install "napari[all]" napari_video pandas
Or, you can use requirements.txt for pip install -r requirements.txt.
This requirements.txt is created in Windows10, python3.9.2 environment.
To start, update config.yaml and then execute python behavior_annotator.py.
1. Press 'F' key on the frame that a behavior starts to set the start flag.
2. Play the video until a behavior ends.
3. Press '1' or '2' key to put the annotations into array.
repeat 1-3, and when all the annotations are done, press '0' key to save the CSV.
other option keys:
-
'3' key: show position of start flag
-
'4' key: delete wrong start flag
-
'5' key: print annotations array
napari contributors (2019). napari: a multi-dimensional image viewer for python. doi:10.5281/zenodo.3555620