Steps to use the code:
- extract videos from incucyte (uncompressed AVI, best quality)
- extract the corresponding object masks as b&w tif images (objects being in white).
- In ImageJ, run the convert_raw_videos.py to create tif stacks from avi files.
- Run extract_intensity.py to extract active object's locations and calcium traces.
- Run your analyses (for an example see display_traces.py)