I'm running some behavioral trials on captive fish, like open field test, mirror test and novel object test. I'd like to analyse the data using video tracking software to get information about fish activity, area used, proximity to an object, etc. I'd appreciate any suggestion of a free software that helps me with this task, e.g., by providing me the coordinates of the fish track over the time. Thanks.
You may wish look at http://recode.net/2014/03/05/crowdsourcing-conservation-microsoft-releases-free-tool-for-tracking-animals/
Thanks Valentin, it seems a great help. I have to read about it.
Dear David, you colud try also CowLog free soft, I've heard it is quite good
http://cowlog.org/
I'd be very interested in hearing how well ZooTracer has been working for anyone.
Zootracer does not run in my computer after having installed it and all the files needed from opencv...any idea?
MOuse lab tracker from this link is good http://www.neuro.ufrn.br/incerebro/mouselabtracker.php
Alos have a look to the Image J plugin WrmTracker
http://www.phage.dk/plugins/wrmtrck.html
Hi David, What did you end up using? I am doing a similar captive species study.
IDtracker is pretty amazing and may be a good fit (http://www.idtracker.es/). Otherwise have a look at ctrax (http://ctrax.sourceforge.net/). I have designed a video tracking tool called BEMOVI, not sure though whether it will work well on fish. You can have look here: http://bemovi.info/ Hope this helps!
Like Frank noted, idTracker or Ctrax are good candidates. I have limited experience in using them, but have tested both briefly. I think idTracker is much easier to start working with. However, you will need to be able to analyse raw data from idTracker, as there is no summary analyses to use yet...
Morten, maybe Noldus "technology" may help you:
http://www.noldus.com/animal-behavior-research/solutions/zebrafish
Best,
António
I know this question was asked 3 years ago, but I needed a software to track some fish and happened across this thread. I tried idtracker, ctrax, and zootrack, but the only one that was able to work with an updated OS was CowLog. I'm not proficient in coding, but it was a pretty understandable interface, and it worked better working with my video in VLC rather than Windows Media Player.
I suggest using the new and userfriendly (and free!!) behavioral analysis tool ToxTrac.
Download it and try it out at: https://sourceforge.net/projects/toxtrac/
/Tomas
I am interested in using IDTracker for my work with juvenile salmon but I am having trouble determining what data you can actually get out of it. It is also much the same problem with the other programs suggested in this thread. I want to look at location in tank, swim speed, shoaling distance, and freezing behaviours. What program can I use to get this data?
Anyone knows how the idTracker is useful in getting the data in zebrafish such as speed, distance travelled, pause, bouyance or swimming behaviour, etc.?
Hi all, @vivekhsridhar from the Max Planck in Konstanz recently developed a free tracking software called Tracktor. Check it out here (with examples in fish, spiders and termites): https://github.com/vivekhsridhar/tracktor
We haved used it to track fast-start escape responses at 1000 fps in small gobies (~20 mm) and it worked like a charm.
Vivek has example videos on the welcome page of his website: https://vhsridhar.wordpress.com/
I'm sure he would be happy to get feedback/questions from any potential users. I'm trying to convince him to write a short methods paper outlining what the software does. Would there be any interest in such a paper or do people find that there are already enough decent free tracking software options out there?
Roche, Thanks for the github information. Does it work on Windows OS. I have downloaded the software but do not know how to install. Could you please explain how to install in Windows10?
The installation instructions have been added to the readme.md file
Hi Dominique, this software seems great, thank you. I want to know whether this tracking software can detect the CM position automatically, or you stick some markers on the fish to track the CM. I have used this software (http://ymnk13.github.io/UMATracker/), and it woks fine in an ideal situation (without wave, and enough contrast), but the wave disturbed the tracking...
Hi Yuuki, no there is no need to mark the fish's CoM. The tracking algorithm automatically determines the CoM based on the outline of the fish's body. Have a look at the single_fish example and/or the video of a goby being tracked on Vivek's website: https://vhsridhar.wordpress.com/ . Waves will always disturb tracking because they cause distortions of the image, so any software (or manual tracking, for that matter) will struggle if the fish is very close to a disturbance at the surface of the water. The tracking algorithm is pretty good, even when colour differences and contrast are not ideal.
Wow, this is really great! Thank you so much. I will try whether this system works for my videos.
FYI - Simon Gingins, Vivek Sridhar and I are working on a detailed tutorial allowing users to easily download the software and run Tracktor smoothly. It should be finished within two weeks or so and Vivek will post it on Github along with all the other files. I'll make sure to post a link here as well.
Almost!! We are working on it at the Max Plank in Konstanz right now. I'll post something here as soon an independently tested version is on GitHub - hopefully in the next few days. If you would like to test the trial version, please email me (dominique.roche [at] unine.ch) and I will gladly send it to you. We would love to have people try it out to let us know if there are any bugs.
We have now posted a detailed user manual for Tracktor on GitHub:
https://github.com/vivekhsridhar/tracktor
Several people have tested the software and it should run smoothly. There are two sections to the user manual: how to install and how to use Tracktor. In section 2, we explain how to run the three examples provided to familiarize yourself with Tracktor and then how to run the software on your own videos.
We have implemented summary statistics for the first example (fish fast-start escape response) and will soon do so for the other two (2 spiders, 8 termites). We are also planning on adding at least one other example that can be modified to suit people's needs.
Feedback for improvements is welcome and/or to notify us of any issues.
vsridhar(at]orn.mpg.de
sgingins(at]orn.mpg.de
dominique.roche(at]unine.ch
The paper for Tracktor is also now available as a preprint on bioRxiv:
https://www.biorxiv.org/content/early/2018/09/09/412262
And the promo video, here: https://twitter.com/vivekhsridhar/status/1039096831236562945
I am about to learn how to automate coding of behavior videos with juvenile Dungeness crabs. I am very interested in Tracktor, thank you very much for sharing this resource! Can anyone who has some experience with tracking programs comment on how using Tracktor might compare with using Image J, the MTrack2 plugin, and then automating speed calculations using R programming language? I need to track position of the crab in the arena, and calculate average speeds on different sides of the arena.
David Villegas-Ríos Daniel S. Hayes Erica Street
We offer a secure cloud-based app that allows you to automate your animal behavioral research.
It can be accessed anywhere in the world by a computer, smartphone, or tablet without downloading anything.
Wouldn't it be amazing to do your behavioral analysis in front of the TV watching Netflix...
You don't need anything fancy in order to get started, typically you can set up your smartphone, and let it record, while you're in a separate room. There is no fear of an interruptance caused by a researcher, etc.
Although we are not an open-source program. Our prices are very competitive when compared to Noldus' EthoVision. You can even share your data with your collaborators.
Please feel free to start your free trial at www.behaviorcloud.com or email me at [email protected] for more details.
You can try the current version of ToxTrac, a free software with tons of functions. Such as support for calibration, multiple arenas, multiple animals per arena or data analysis.
Website and download: https://toxtrac.sourceforge.io
Instruction video: https://youtu.be/RaVTsQ1JwfM
Publications:
- Rodriguez, A., Zhang, H., Klaminder, J., Brodin, T., Andersson, P. L. and Andersson, M. (2018). ToxTrac: a fast and robust software for tracking organisms. Methods in Ecology and Evolution. 9(3), 460-464.
- Rodriguez, A., Zhang, H., Klaminder, J., Brodin, T., and Andersson, M. (2017). ToxId: an algorithm to track the identity of multiple animals. Scientific Reports. 7(1):14774.
Hope some of you will find it useful.
We have been working on it for a long time, and I expect we can further improve it and make ir better
You should try DeepLabCut!
It´s an open source Deep Learning software that works really good once you get used to it:
https://github.com/AlexEMG/DeepLabCut/blob/master/docs/installation.md
I have used tracktor (and cited) for monitoring chicken behaviour in tests.
(Article Relationship between Range Use and Fearfulness in Free-Range...
) It worked really well and by adding an ellipse to enclose the shape determined bevaviours in static chickens as well as moving chickens.
For those using Windows OS, there is also AnimalTA: http://vchiara.eu/index.php/animalta
It's free and user-friendly (no need to code, easy installation). It allows tracking a high number of targets in the same or in multiple arenas. It's specially adapted to "difficult" videos (low resolution, tremors, changes in lighting conditions, etc.). It does both tracking and trajectory analyses.