The document presents a non-invasive method for measuring physical activity in rats using frame difference analysis of video tracking without markers. The method, called Gemvid, uses commodity hardware and free, open-source software. It was validated through theoretical tests and comparison to an Actiwatch device, and proved accurate for monitoring rats' circadian rhythms over multiple days. The key advantages are low cost, non-invasiveness, reproducibility, stability, and the ability to use freely available tools.

1. Activity measurement
Our solution
Validation
Conclusions
Animal monitoring with Gemvid
Non-invasive measure of rats physical global activity
Jean-Etienne & Laurent Poirrier
CNCM, CRC & SystMod
University of Liege
February 7th, 2009
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

2. Activity measurement Running wheel
Our solution Radar
Validation Video tracking
Conclusions Body markers
How to measure rats physical activity? Running wheel?
What should you do when your mouse or rat is out of the running wheel?
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

3. Activity measurement Running wheel
Our solution Radar
Validation Video tracking
Conclusions Body markers
How to measure rats physical activity? Radar?
Do you really want such a complicated hardware?
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

4. Activity measurement Running wheel
Our solution Radar
Validation Video tracking
Conclusions Body markers
How to measure rats physical activity? Video tracking?
Good idea but costly and impractical (center of gravity only)
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

5. Activity measurement Running wheel
Our solution Radar
Validation Video tracking
Conclusions Body markers
How to measure rats physical activity? Markers?
Rats don’t like it ...
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

6. Activity measurement
Frame difference analysis
Our solution
Gemvid setup
Validation
Technics
Conclusions
Quantification of overall free movements of rodents
without any markers,
using a commercially available CCTV
and modular, free software
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

7. Activity measurement
Frame difference analysis
Our solution
Gemvid setup
Validation
Technics
Conclusions
Frame difference analysis, roughly
1
Each s, a photo of the animal is taken and compared to the previous one.
25
We compute the number of pixels that are different.
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

8. Activity measurement
Frame difference analysis
Our solution
Gemvid setup
Validation
Technics
Conclusions
Gemvid
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

9. Activity measurement
Frame difference analysis
Our solution
Gemvid setup
Validation
Technics
Conclusions
Hardware & Software
any camera (IR if needed)
(Lianyida-806C, 60 EUR)
any video4linux-enabled
framegrabber (ATI Rage 128
AIW, 5 EUR)
any computer running Linux
(PII 350MHz, 35 EUR)
E-bay is your friend!
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

10. Activity measurement
Frame difference analysis
Our solution
Gemvid setup
Validation
Technics
Conclusions
Hardware & Software
any camera (IR if needed) GNU/Linux (RedHat v7.3)
(Lianyida-806C, 60 EUR) video4linux API (direct ioctl)
any video4linux-enabled no other dependencies
framegrabber (ATI Rage 128
ASCII output (need a pipe
AIW, 5 EUR)
anyone?)
any computer running Linux
data visualisation with GD,
(PII 350MHz, 35 EUR)
MatlabScilab, PIL, ...
E-bay is your friend!
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

11. Activity measurement Theoretical validation
Our solution Publication
Validation Comparison with Actiwatch
Conclusions Working with rats
“Theoretical” validation
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

12. Activity measurement Theoretical validation
Our solution Publication
Validation Comparison with Actiwatch
Conclusions Working with rats
“Theoretical” validation
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

13. Activity measurement Theoretical validation
Our solution Publication
Validation Comparison with Actiwatch
Conclusions Working with rats
Publication
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

14. Activity measurement Theoretical validation
Our solution Publication
Validation Comparison with Actiwatch
Conclusions Working with rats
Comparison with an Actiwatch
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

15. Activity measurement Theoretical validation
Our solution Publication
Validation Comparison with Actiwatch
Conclusions Working with rats
Working with rats (finally)
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

16. Activity measurement Theoretical validation
Our solution Publication
Validation Comparison with Actiwatch
Conclusions Working with rats
Rat during the day
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

17. Activity measurement Theoretical validation
Our solution Publication
Validation Comparison with Actiwatch
Conclusions Working with rats
Rat during the night
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

18. Activity measurement Theoretical validation
Our solution Publication
Validation Comparison with Actiwatch
Conclusions Working with rats
Rats circadian rhythm
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

19. Activity measurement
Our solution
Validation
Conclusions
Conclusions
Sensitive
1
Reproducible
2
Stable over time
3
More accurate
4
than actiwatch
Proven with
5
rodents
Non-invasive
6
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

20. Activity measurement
Our solution
Validation
Conclusions
And more importantly ...
Use commodity hardware
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

21. Activity measurement
Our solution
Validation
Conclusions
And more importantly ...
Use commodity hardware
Free as in “Free beer”
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

22. Activity measurement
Our solution
Validation
Conclusions
And more importantly ...
Use commodity hardware
Free as in “Free beer”
Free as in “Free speech”
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

23. Activity measurement
Our solution
Validation
Conclusions
Many thanks to
Professors G. Moonen & A. F.R.I.A.
Luxen Fonds Leon Fredericq
Drs. P. Leprince & P. Maquet B.A.S.S. & C.E.T.E.S.
As well as all the rats that calmly
participated in all my experiments
And thanks to you for your attention!
http://www.bioinformatics.org/gemvid
http://dx.doi.org/10.1186/1740-3391-4-10
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

24. Activity measurement
Our solution
Validation
Conclusions
1. Sensitivity & Reproducibility
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

25. Activity measurement
Our solution
Validation
Conclusions
Comparison with a fixed oscillator
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

26. Activity measurement
Our solution
Validation
Conclusions
2. Stability over time
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

27. Activity measurement
Our solution
Validation
Conclusions
Stability over time
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

28. Activity measurement
Our solution
Validation
Conclusions
3. Comparison with an existing device
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

29. Activity measurement
Our solution
Validation
Conclusions
Comparison with an Actiwatch
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

30. Activity measurement
Our solution
Validation
Conclusions
Working with rats (finally)
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

31. Activity measurement
Our solution
Validation
Conclusions
Rats circadian rhythm
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

32. Activity measurement
Our solution
Validation
Conclusions
Rats circadian rhythm
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid