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.
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.
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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