Hi,
I have to visualize a batch of videos of fish behaviour in captivity and extract some variables from them. These are for example: total time active, total time motionless, total time in a particular region, number of attacks to a model prey,number of bites, etc...
I can do it manually viewing the videos as many times as variables I need to extract, but this will very time-consuming. I wonder if there is any software that can help me with this task. What I need is to be able to watch the video once, and record all the important events at the same time (sort of ethogram...).
Could anyone suggest any software or give any advise?
Many thanks!
Hi,
You should try Solomon coder, which you cen get and try for free.
http://solomoncoder.com
Hi,
You should try Solomon coder, which you cen get and try for free.
http://solomoncoder.com
this free software does some things automatically but I am not sure is what you want.
swistrack -> http://sourceforge.net/projects/swistrack/
So if you want to do things manually I think a very good one (is also free) is Jwatcher. a bit tricky in setting up (read the instructions and you won't have issues) but very useful.
Jwatcher -> http://www.jwatcher.ucla.edu/
Great! I've playing with both of them and Solomon seems much easier to configure. It seems it exactly does what I need.
Thanks!
It seems you are wanting to record multiple parameters of fishes in captivity in response to food, hunger, chemicals, pollutants etc. etc. in a video form so that you can record multiple parameters at the same time to derive a conclusive behavioral activity paradigm.
A system that combines the sensitivity of a behavioral assay of the fish in captivity with commercially available automated monitoring equipment consists of a special aquarium coupled to a recirculating water system, and an Opto-Varimex-Aqua activity tracking meter (Columbus Instruments, Columbus, Ohio) interfaced to a microcomputer. The tracking meter forms an intersecting, planar grid of light beams which, when interrupted by fish movements, is translated into a digitized signal and fed to the computer. The assay is based on the response of fish to natural chemical stimuli such as food odors or pheromones. When these stimulus solutions are injected into the water circulation the response of the fish is monitored by the computer system, which is capable of discriminating and quantifying changes in eight parameters. Normal responses to stimuli are compared with the response of fish that have been exposed to pollutants. The system should be easily adapted to any laboratory concerned with testing for effects of toxic substances, and will identify effects of pollution that have thus far been difficult or impossible to assess.
Good Luck David.
If you are looking for freeware there's also JWatcher. I've used it myself and it works pretty well.
Thanks. I'm working with Solomon and it performs pretty well!
David
Hi, i am using Jwatcher, it is free and pretty simple to use it. Blumstein et al. Create it
Maybe other software developed by Noldus corporation is better than EthoVision for this purpose - The Observer XT. But it is also licensed.
You can try JWatcher. Unlike Noldus software, its freeware and it works pretty well. However, if you have many variables you might not be able to extract all of them by watching the video only once. Ultimately it will depend on how fast your animals are moving/changing between behavioural elements and how good you are using the keyboard to score them.
I would also recommend J watcher. Alternatively, depending on what you have to do, Swistrack is another software that allows to automatically detect moving shapes on a homogeneously colored background. The software allows background subtraction from a template image in order to improve shape detection and many other minor tweaks. It's very handy to measure motility of fishes or insects in small arenas since it allows the simultaneous detection of multiple objects, although not always easily.
recently this has been developed for mice (works in a similar way)
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0074557
check also
http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1924.html
I use this software named etholog. You can record the behaviours like instant events or measure duration time of each behaviour. It is free, simple and efficient !
http://www.ip.usp.br/docentes/ebottoni/EthoLog/ethohome.html
Again, depending on how much movement there is in your videos, we have developed a program ('wevers') to automatically score when something moves, which might be useful for you. Although this has been developed for birds visiting nests, it can be applied to other systems as well. The program will analyse your videos for you and give you a txt file with all the times when something happened, which can then be used to check on identity of individuals and/or specific behaviour. Sensitivity can be adjusted.
See the below link for more information:
http://revandijk2.wordpress.com/publications/
Try also BehaView it is a very easy in use and most of all free software.
http://www.pmbogusz.net/software/behaview/
Hi, we are using the software InterAct (not free) and SolomonCoder (free). There is a trial version for InterAct. Depending on how detailed you want the output analysis to be InterAct is a very good software to analyse videos. The SonlomonCoder does allow you to code your events on the video in a very easy way but any further analysis must be 'hand-made'.
Thanks, I'm actually using Solomon coder and it works pretty well for what need.
Solomon is very good and is quite easy to learn...so would definitely recommend using this.
We developped BORIS an easy-to-use event logging software for video/audio coding or living observation. BORIS is a free and open-source software available for GNU/Linux, Windows and Mac OS X.The major features are:
* Coding and describing visual and audio information using an integrated playback
* Frame-by-frame mode
* Configuration of unlimited number of subjects and behaviors
* Definition of an unlimited number of independent variables
* Up to 2 media file can be synchronously played
* Coding of media files at various playback speeds
* Media files can be enqueue for playing, the event time will be the cumulative over all media.
* Time budget analysis
* Graphical representation of coded data
* Exporting coded data in various formats (TSV, CSV, ODS, XLS)
* Geometric measurements
See http://penelope.unito.it/boris for details
I need the same. I will try use this programs to do a ethogram of Gymnorhamphichthys rondoni, a electric fish in field and captivity.
I am linking the following thread so that those interested in ethogram/behavioral inventory software can see similar conversations (I have done the same for that thread as well):
https://www.researchgate.net/post/Are_there_any_open-sourced_options_alternatives_to_behavioral_observation_scoring_software?isAnswerFieldFocused=true
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