Activity measurementOur solution
ValidationConclusions
Animal monitoring with GemvidNon-invasive measure of rats physical global activity
Jean-Etienne & Laurent Poirrier
CNCM, CRC & SystModUniversity of Liege
February 7th, 2009
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Running wheelRadarVideo trackingBody 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
Activity measurementOur solution
ValidationConclusions
Running wheelRadarVideo trackingBody markers
How to measure rats physical activity? Radar?
Do you really want such a complicated hardware?
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Running wheelRadarVideo trackingBody 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
Activity measurementOur solution
ValidationConclusions
Running wheelRadarVideo trackingBody markers
How to measure rats physical activity? Markers?
Rats don’t like it ...
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Frame difference analysisGemvid setupTechnics
Quantification of overall free movements of rodentswithout any markers,
using a commercially available CCTVand modular, free software
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Frame difference analysisGemvid setupTechnics
Frame difference analysis, roughly
Each 125
s, a photo of the animal is taken and compared to the previous one.We compute the number of pixels that are different.
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Frame difference analysisGemvid setupTechnics
Gemvid
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Frame difference analysisGemvid setupTechnics
Hardware & Software
any camera (IR if needed)(Lianyida-806C, 60 EUR)
any video4linux-enabledframegrabber (ATI Rage 128AIW, 5 EUR)
any computer running Linux(PII 350MHz, 35 EUR)
E-bay is your friend!
GNU/Linux (RedHat v7.3)
video4linux API (direct ioctl)
no other dependencies
ASCII output (need a pipeanyone?)
data visualisation with GD,MatlabScilab, PIL, ...
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Frame difference analysisGemvid setupTechnics
Hardware & Software
any camera (IR if needed)(Lianyida-806C, 60 EUR)
any video4linux-enabledframegrabber (ATI Rage 128AIW, 5 EUR)
any computer running Linux(PII 350MHz, 35 EUR)
E-bay is your friend!
GNU/Linux (RedHat v7.3)
video4linux API (direct ioctl)
no other dependencies
ASCII output (need a pipeanyone?)
data visualisation with GD,MatlabScilab, PIL, ...
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Theoretical validationPublicationComparison with ActiwatchWorking with rats
“Theoretical” validation
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Theoretical validationPublicationComparison with ActiwatchWorking with rats
“Theoretical” validation
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Theoretical validationPublicationComparison with ActiwatchWorking with rats
Publication
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Theoretical validationPublicationComparison with ActiwatchWorking with rats
Comparison with an Actiwatch
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Theoretical validationPublicationComparison with ActiwatchWorking with rats
Working with rats (finally)
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Theoretical validationPublicationComparison with ActiwatchWorking with rats
Rat during the day
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Theoretical validationPublicationComparison with ActiwatchWorking with rats
Rat during the night
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Theoretical validationPublicationComparison with ActiwatchWorking with rats
Rats circadian rhythm
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Conclusions
1 Sensitive
2 Reproducible
3 Stable over time
4 More accuratethan actiwatch
5 Proven withrodents
6 Non-invasive
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
And more importantly ...
Use commodity hardware
Free as in “Free beer”
Free as in “Free speech”
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
And more importantly ...
Use commodity hardware
Free as in “Free beer”
Free as in “Free speech”
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
And more importantly ...
Use commodity hardware
Free as in “Free beer”
Free as in “Free speech”
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Many thanks to
Professors G. Moonen & A.Luxen
Drs. P. Leprince & P. Maquet
F.R.I.A.
Fonds Leon Fredericq
B.A.S.S. & C.E.T.E.S.
As well as all the rats that calmlyparticipated 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
Activity measurementOur solution
ValidationConclusions
1. Sensitivity & Reproducibility
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Comparison with a fixed oscillator
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
2. Stability over time
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Stability over time
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
3. Comparison with an existing device
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Comparison with an Actiwatch
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Working with rats (finally)
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Rats circadian rhythm
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid
Activity measurementOur solution
ValidationConclusions
Rats circadian rhythm
Jean-Etienne & Laurent Poirrier Animal monitoring with Gemvid