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3D-ZeF20 - Zebrafish challenge

3DZeF_PIC

Requirements

Usage

  1. Run
python ZF3D/evalZF3D.py

Evaluation

To run the evaluation for your method please adjust the file ZF3D/evalZF3D.py using the following arguments:

benchmark_name: Name of the benchmark, e.g. ZeF-3D
gt_dir: Directory containing ground truth files in <gt_dir>/<sequence>/gt/gt.txt
res_dir: The folder containing the tracking results. Each one should be saved in a separate .txt file with the name of the respective sequence (see ./res/data)
save_pkl: path to output directory for final results (pickle) (default: False)
eval_mode: Mode of evaluation out of ["train", "test", "all"] (default : "train")

eval.run(
    benchmark_name = benchmark_name,
    gt_dir = gt_dir,
    res_dir = res_dir,
    eval_mode = eval_mode)

Visualization

To visualize your results or the annotations run python ZF3D/ZF3DVisualization.py

Inside the script adjust the following values for the ZF3DVisualizer class:

seqName: Name of the sequence
FilePath: Data file
image_dir: Directory containing images
mode: Video mode. Options: None for method results, raw for data video only, and gt for annotations
output_dir: Directory for created video and thumbnail images

Additionally, adjust the following values for the generateVideo function:

displayTime: If true, display frame number (default false)
displayName: Name of the method
showOccluder: If true, show occluder of gt data
fps: Frame rate

visualizer = ZF3DVisualizer(seqName, FilePath, image_dir, mode, output_dir )
visualizer.generateVideo(displayTime, displayName, showOccluder, fps  )

Data Format

Submit your tracking result where each row of your submission file has to contain the following values. The values are defined as in the annotation file, and any other values will be ignored.
Each line of an annotation txt file is structured as follows:

frame: The video frame which the annotation is associated with 
id: Identity of the fish
3d_x: x coordinate of 3D head position in world coordinates
3d_y: y coordinate of 3D head position in world coordinates
3d_z: z coordinate of 3D head position in world coordinates

Four example lines of a submission txt file:

1, 1, 19.61, 28.313, 7.93
1, 2, 18.317, 28.636, 8.911
2, 1, 19.685, 28.348, 7.886
2, 2, 18.197, 28.625, 8.868

Citation

If you work with the code and the benchmark, please cite:

@article{3DZeF20,
    title={3D-ZeF: A 3D Zebrafish Tracking Benchmark Dataset},
    shorttitle = {3DZeF20},
	url = {https://arxiv.org/abs/2006.08466},
	journal = {arXiv:2006.08466[cs]},
	author={Malte Pedersen and Joakim Bruslund Haurum and Stefan Hein Bengtson and Thomas B. Moeslund},
	year = {2020},
	note = {arXiv: 2006.08466},
	keywords = {Computer Science - Computer Vision and Pattern Recognition}

}

Contact

If you find a problem in the code, please open an issue.

For general questions, please contact Joakim Bruslund (joha@create.aau.dk) or Malte Pedersen (mape@create.aau.dk)