I have only worked with EthoVision up until now so I don't know if there is a better alternative. Recently I found ilastik but didn't have the time to test it out. It sounds really promising and it is open source.

http://ilastik.org/

Maybe someone here already has experience working with it and can elaborate.

Dear Philipp, Ilastik looks really interesting. Let's wait for other people impression as to how they see differences between Noldus EthoVision and Ilastik. 

Here are 3 freeware solutions I found in another thread (2 especially for Drosophila):

http://buridan.sourceforge.net/

http://ctrax.sourceforge.net/

https://en.wikibooks.org/wiki/SwisTrack

ctrax looks terrific! Thank you very much! I hope to try it next week. I'll let you know my impression. 

Ethovision has worked for us, but it takes a lot of troubleshooting and optimization (several months) that the technical support at the company was really unable to help with. Its been the same experience with other users of the system I have talked to regarding tracking flies.

Hi there, I would take a look at idTracker - it's a free tracking software that can track one or more individuals that are unmarked. It requires a bit specific lighting conditions but their methods paper used it to track multiple fruit flies so it should be applicable. 

http://www.idtracker.es/home

I think they recently sold it as well to Ethovision and is being incorporated into their next version of the software. 

Dear Charles, Thank you very much! Your story about technical complications sounds alarming. Best wishes, Indrikis

Thank you Paul. idTracker is designed for PC. I'll try to find one and test asap. 

We have tested idTracker, but there was a lot of problem with this software. We are still using swistrack.I think, with a good recording software (like VirtualDub) swistrack is very usefull tool. ST gives raw data with objects coordinants in time. With this type of data we can do whatever we want (for example analyse in R).

Dear Jacek, 

Thank you very much for your response! I must look Swistrack and VirtualDub. What kind of data you can retrieve from your system? And how you export these to R?

We have excellent experience with Ethovision for tracking of thrips and aphids; Noldus IT provides valuable support to its users. I cannot compar to other systems.

Dear Marcel, 

Many people say warm words about Noldus system, and also here at the University of Tennessee where I am at the moment. They also say that the system requires much time to be properly adjusted. Do you do this part yourself or you have a skillful technician available? Thank you! Indrikis

From SwissTrack you get raw data with objects coordinants in time. Than you can import it to R. What data you will get from it in R deppends of what analysis (package; we are uding habitat) you choose (rest time, distance, space usage, turning angle and other). This way of analysis is not so comfortable as EthoVision but you can control the whole analysis process and you can change it if you want. I heard different opinions about EthoVision, I have been using it few times on basic level. In my lab we had no found to buy it so we decided to develop our system, where we can control whole analysis process.    

Have anybody ever tried to use the behavioral sequences obtained by EthoVision, SwissTrack or other software to see whether these are described by Markov chains or by non-Markovian dynamics?

I have found specialized package for R to analise Markov dynamics. http://cran.r-project.org/web/packages/markovchain/vignettes/an_introduction_to_markovchain_package.pdf  OR http://www.jstatsoft.org/v42/i09/paper . I didnt use it but it should work with ST data. 

Jacek, thank you! I highly appreciate this. 

something new for me: BORIS http://boris.readthedocs.io/en/latest/# , in my opinion hugh functionality when compare with EthoViosion

We have developed a free software for animal tracking, we have tried it with fish, insects and rodents, you can download it at https://toxtrac.sourceforge.io

We would appreciate it if you try it and email me any feedback

https://toxtrac.sourceforge.io

Indrikis Krams We have developed an affordable option compared to Noldus, Anymaze, Cleversys, and allows you to access from any device as well as share with colleagues and collaborators. We also provide great technical support, training, and consulting services as well. Please check us out at www.behaviorcloud.com