Journal article Open Access
Brian Q. Geuther;
Sean P. Deats;
Kai J. Fox;
Steve A. Murray;
Robert E. Braun;
Jacqueline K. White;
Elissa J. Chesler;
Cathleen M. Lutz;
Vivek Kumar
Both the training data and trained models used in the paper are found here.
Dataset description
Information for each dataset falls into 3 folders. Filenames portray the dataset split used in the paper that they belong to (eg Training_1.png or Validation_1.png).
Trained Model Description
We also release models trained on all the subsets of training data we share. Each trained model was trained using our code over on Github: https://github.com/KumarLabJax/MouseTracking
Brief descriptions of the training subsets
Please read the associated paper for additional detail. A brief summary of the environment is added here:
Standard Open Field Strain Survey
We annotated 16234 training and 568 validation images of a single mouse in the same open field. The mouse can be one of multiple coat colors, but visually appears as a black, light-grey, or white color. In the case the mouse’s posture created a poor ellipse-fit, portions of the mouse were removed (such as tail) to enable a good ellipse-fit.
24Hr Open Field Dataset
We annotated 2099 training and 93 validation images of a single mouse in the same open field listed above augmented with bedding and a food container. All mice in this experiment appear black on video. There are 2 states, with visible light and with only infrared. The infrared-only imaging contains much higher visual noise.
KOMP Open Field Dataset
We annotated 1000 training and 83 validation images of a single mouse in JAX’s KOMP2 open field arena. All mice have a black coat color.
Test Ground Truth Dataset
To test the robustness of our system against conventional trackers that build a background model from multiple frames in a video, we re-sampled video a 20 minute video at 1 frame per second and annotated all the resulting frames (1179-1200 frames). We did this for the 6 environments in the paper of varying difficulty (Black, Gray, Piebald, Albino, 24Hr, KOMP2). The format of this data follows a DataSubset_FrameNumber format instead of Training/Validation_FrameNumber format.
Name | Size | |
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24Hr_Dataset.tar
md5:22e43adf5463eac584020909cb7d4638 |
565.9 MB | Download |
KOMP_Dataset.tar
md5:d6387eb0c3c82bc3d59bde753b3539c3 |
184.2 MB | Download |
OFA_Dataset.tar
md5:01f20fc35883f42d26cfb1e9088cf7a4 |
1.9 GB | Download |
Pretrained_Models.tar
md5:695ebca1fd03d783069ab7205d9bd790 |
660.7 MB | Download |
TestGT_Dataset.tar
md5:a3762f2c45c7fe36ae5d06cb1bf48a2e |
1.5 GB | Download |
Geuther, Brian Q., et al. "Robust mouse tracking in complex environments using neural networks." Communications biology 2.1 (2019): 1-11.
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