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Data from: Quantifying influence of human choice on the automated detection of Drosophila behavior by a supervised machine learning algorithm

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Data from: Quantifying influence of human choice on the automated detection of Drosophila behavior by a supervised machine learning algorithm

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1 digital object.

Cite This Work

Leng, Xubo; Wohl, Margot; Ishii, Kenichi; Nayak, Pavan; Asahina, Kenta (2020). Data from: Quantifying influence of human choice on the automated detection of Drosophila behavior by a supervised machine learning algorithm. UC San Diego Library Digital Collections. https://doi.org/10.6075/J0QF8RDZ

Description

This dataset contains all the movie files, derivative files generated by FlyTracker and JAABA, and all the behavior classifiers described in our article (Leng, X., et al., 2020). In other words, there are raw data which could not be included in the article due to space limitations. With our custom codes (available at https://github.com/asahinak/Leng_Wohl_etal_2020_JAABA_vs_human_annotation), readers can reproduce all the results presented in the article.

Contents:

There are 3 groups of files. The first contains the classifiers, and the second contains files associated with movies that capture fly behaviors. The third is a single file, ‘featureConfigEyrun.xml’, which is required for JAABA to read outputs of FlyTracker.

1) Classifiers

Classifiers for each of lunges, headbutts, and wing extensions are organized into 3 separate directories. The first is “[behavior name]_PartialTraining” directory, the second is “[behavior name]_Downsampled” directory, and the third is “[behavior name]_SelectFeatures” directory.

A PartialTraining directory contains 4 .JAB classifiers that were trained with only a subset of the complete training frames, along with a classifier trained with all available frames (total 5 classifiers). The number at the end of the file name corresponds to the number of classifiers described in Supplementary Table S6. See Fig. 4 of the article for the performance evaluations of these classifiers, and Supplementary Tables S1-S4 for details of training frames.

A Downsampled directory contains 50 .JAB classifiers that were trained with downsampled training frames. Ten classifiers trained with randomly chosen training frames (described in details in Supplementary Table S6 the article) were generated for each of 5 downsampling rates. See Fig. 4 and Supplementary Fig. S4 of the article for the summary of downsampled classifiers’ performance.

A SelectFeatures directory contains 8 .JAB classifiers that were trained with selected features or rules. See Fig. 5 and Supplementary Fig. S5 of the article for the performance evaluations of these classifiers, and Supplementary Table S5 of the article for the details of features or rules that were selectively eliminated.

2) Movies and associated files

One .AVI movie and associated files are grouped into one .ZIP file. See Table 1 and Supplementary Table S1 of the article for detailed metadata, such as genotypes of the flies, experimental conditions, and fly pairs used for classifier training and performance evaluation. The extracted file has a nested directory structure along with various files in each subdirectory. It is important to maintain the directory structure for FlyTracker and JAABA to operate properly. For details of these programs, please see the following link and documentation:

FlyTracker: http://www.vision.caltech.edu/Tools/FlyTracker/
(Reference: Eyjolfsdottir, E. et al. (2014) Detecting social actions of fruit flies. In: Fleet D., Pajdla T., Schiele B., Tuytelaars T. (eds) Computer Vision – ECCV 2014. ECCV 2014. Lecture Notes in Computer Science, vol 8690. Springer, Cham. https://doi.org/10.1007/978-3-319-10605-2_50)

JAABA: http://jaaba.sourceforge.net/
(Reference: Kabra M. et al., JAABA: interactive machine learning for automatic annotation of animal behavior. Nat Methods 10, 64–67 (2013). https://doi.org/10.1038/nmeth.2281)

The base directory contains the following 3 components:
- An .AVI movie ([movie_name].avi): an original movie of behaving fly pairs.
- calibration.mat file: created during calibration step of FlyTracker.
- A [movie_name] subdirectory

The [movie_name] subdirectory contains the following 4 components:
- A [movie_name]-bg.mat file: a background file created by FlyTracker.
- A [movie_name]-feat.mat file: a feature file created by FlyTracker
- A [movie_name]-track.mat file: a tracking file created by FlyTracker
- A [movie_name]_JAABA subdirectory

The [movie_name]_JAABA subdirectory contains the following 2 components:
- A trx.mat file: JAABA’s tracking file
- A ‘perframe’ subdirectory

The perframe subdirectory contains 39 JAABA features (.mat) as described in Eyjolfsdottir et al. (see above) and Fig. 2 of the article.

Note that we removed a “movie.avi” file under the [movie_name]_JAABA subdirectory to reduce the file size. Copy the original movie into this subdirectory, and rename the file to “movie.avi” if you wish to visualize the movie in the JAABA training mode.

3) featureConfigEyrun.xml

This file is kindly provided by Eyrun Eyjolfsdottir in Prof. Pietro Perona’s lab at Caltech. It is necessary for JAABA to create a [movie_name]_JAABA subdirectory with correct perframe feature files from output files of FlyTracker.

When JAABA is installed, copy the featureConfigEyrun.xml file in the ‘JAABA-masterperframeparams’ directory. FlyTracker output files should be readable by JAABA.

Date Collected
  • 2015-03 to 2018-09
Date Issued
  • 2020
Authors
Principal Investigator
Funding

NIGMS R35 GM119844 (to K.A.), the Japan Society for the Promotion of Science (to K.I.), the Naito Foundation (to K.I.), the Mary K. Chapman Foundation (to M.W.), the Rose Hills Foundation (to M.W.)

Scientific Name
Topics

Formats

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Language
  • English
Identifier

Identifier: Kenta Asahina: http://orcid.org/0000-0001-6359-4369

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