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Protocols

JAABA specifications

Information


Unique identifier OMICS_12997
Name JAABA
Alternative name Janelia Automatic Animal Behavior Annotator
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Kristin Branson

Publication for Janelia Automatic Animal Behavior Annotator

JAABA citations

 (7)
call_split

Automated computer based detection of encounter behaviours in groups of honeybees

2017
Sci Rep
PMCID: 5732155
PMID: 29247217
DOI: 10.1038/s41598-017-17863-4
call_split See protocol

[…] o produce the ‘encounter classifier’, we labelled examples of encounter and non-encounter behaviour in 105 minutes of tracking information and video material using the graphical user interface of the JAABA program. We only labelled encounter and non-encounter behaviours for which we had high confidence in classification. Thus, for encounter behaviours we only labelled those for which we could conf […]

library_books

Multiple Drosophila Tracking System with Heading Direction

2017
PMCID: 5298669
PMID: 28067800
DOI: 10.3390/s17010096

[…] ntations of walking flies. The program comes with the ability to automatically classify the flies’ behaviors. In addition to C-Trax, another system that is well-known for measuring animal behavior is JAABA []. JAABA uses a machine learning-based system to compute behavior of animals together with the input trajectory from other tracking programs. idTracker [] provides a tracking system that can be […]

library_books

Searching for motifs in the behaviour of larval Drosophila melanogaster and Caenorhabditis elegans reveals continuity between behavioural states

2015
PMCID: 4707863
PMID: 26609067
DOI: 10.1098/rsif.2015.0899

[…] urs, ESA produced an F-score of 0.72 (precision = 0.67 and sensitivity = 0.77), where the dominant source of error was a large number of false positive run casts. On the same behavioural experiments, JAABA annotation produced an F-score of 0.68 also with many false positive events. See for the precision, sensitivity and F-score statistics for each behaviour for both JAABA annotation and ESA. Elec […]

library_books

Context specific comparison of sleep acquisition systems in Drosophila

2015
PMCID: 4728345
PMID: 26519516
DOI: 10.1242/bio.013011

[…] esearchers from examining multiple animals simultaneously to look at the effects of social interactions on sleep behavior. However, it should be noted that a number of programs, for example ctrax and JAABA, have been developed for the simultaneous tracking of multiple animals within a single arena (; ; ). While these systems provide increased flexibility, they are computationally demanding and are […]

library_books

Analyzing animal behavior via classifying each video frame using convolutional neural networks

2015
Sci Rep
PMCID: 4585819
PMID: 26394695
DOI: 10.1038/srep14351

[…] d more importantly, many interesting behaviors require analyzing sequences of frames. One approach to address this is using the nets’ frame-by-frame classification as an input feature for a tool like JAABA, which focusses on detecting behaviors from sequences of features of frames. With the continuing advances in easily available processing power and CNN technology (e.g.,), however, using neural n […]

library_books

Female mice ultrasonically interact with males during courtship displays

2015
eLife
PMCID: 4447045
PMID: 26020291
DOI: 10.7554/eLife.06203.013

[…] An automated classifier (Janelia Automatic Animal Behavior Annotator; JAABA; , http://jaaba.sourceforge.net) was used for identifying events when a female mouse was being followed. The classifier was trained on 5228 frames of […]

Citations

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JAABA institution(s)
Howard Hughes Medical Institute, Janelia Farm Research Campus (HHMI JFRC), Ashburn, VA, USA; Development, Evolution and the Environment Laboratory, Instituto Gulbenkian de Ciência, Oeiras, Portugal; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
JAABA funding source(s)
All work was funded by the Howard Hughes Medical Institute and the Janelia Farm Research Campus.

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