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Non-invasive animal monitoring with Gemvid

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In this lightning talk for FOSDEM 2009, we will first introduce Gemvid, a system that allows the monitoring of animals in their own environment for an extended period of time. Then, we'll show how we demonstrated the sensitivity, reproducibility and stability of the system. Finally, we'll highlight some issues and interesting points for the future of Gemvid.

Website: http://www.bioinformatics.org/gemvid/

Published in: Technology
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Non-invasive animal monitoring with Gemvid

  1. 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. 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. 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. 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. 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. 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. 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. 8. Activity measurement Frame difference analysis Our solution Gemvid setup Validation Technics Conclusions Gemvid Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  9. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 20. Activity measurement Our solution Validation Conclusions And more importantly ... Use commodity hardware Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  21. 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. 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. 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. 24. Activity measurement Our solution Validation Conclusions 1. Sensitivity & Reproducibility Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  25. 25. Activity measurement Our solution Validation Conclusions Comparison with a fixed oscillator Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  26. 26. Activity measurement Our solution Validation Conclusions 2. Stability over time Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  27. 27. Activity measurement Our solution Validation Conclusions Stability over time Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  28. 28. Activity measurement Our solution Validation Conclusions 3. Comparison with an existing device Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  29. 29. Activity measurement Our solution Validation Conclusions Comparison with an Actiwatch Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  30. 30. Activity measurement Our solution Validation Conclusions Working with rats (finally) Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  31. 31. Activity measurement Our solution Validation Conclusions Rats circadian rhythm Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
  32. 32. Activity measurement Our solution Validation Conclusions Rats circadian rhythm Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid

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