This is Official code of "Cell Detection in Domain Shift Problem Using Pseudo-Cell-Position Heatmap", Miccai 2021
- Python3.7
- PyTorch
- OpenCV
$ python3 main.py --random_seed ${random_seed} --test_path ${test_path} --target_path ${target_path} --source_path ${source_path} --steps ${numbers of domain adaptation}
For implementation, your directory have to be structure like below.
Directory Structure
├── All_fscore.py
├── Data
│ ├── seq2
│ │ ├── gt
│ │ │ ├── seq2_00000_000_000.tif
│ │ │ ├── seq2_00000_000_001.tif
│ │ │ ├── seq2_00000_000_002.tif
│ │ │ │ .
│ │ │ │ .
│ │ │ │ .
│ │ │ │
│ │ │ ├── seq2_00099_007_006.tif
│ │ │ ├── seq2_00099_007_007.tif
│ │ │ ├── seq2_00099_007_008.tif
│ │ │ └── seq2_00099_007_009.tif
│ │ └── ori
│ │ ├── seq2_00000_000_000.tif
│ │ ├── seq2_00000_000_001.tif
│ │ ├── seq2_00000_000_002.tif
│ │ ├── seq2_00000_000_003.tif
.
.
.
│ │ ├── seq2_00099_007_006.tif
│ │ ├── seq2_00099_007_007.tif
│ │ ├── seq2_00099_007_008.tif
│ │ └── seq2_00099_007_009.tif
│ └── test_seq6
│ ├── gt
│ │ ├── 00000.tif
│ │ ├── 00001.tif
│ │ ├── 00002.tif
.
.
.
│
│ │ ├── 00098.tif
│ │ └── 00099.tif
│ └── ori
│ ├── 00000.tif
│ ├── 00001.tif
.
.
.
│ ├── 00098.tif
│ └── 00099.tif
├── Detection
│ ├── detection
│ │ ├── custom_loss.py
│ │ ├── detection_eval.py
│ │ ├── __init__.py
│ ├── fscore.py
│ ├── networks
│ │ ├── __init__.py
│ │ ├── network_model.py
│ │ ├── network_parts.py
│ ├── predict.py
│ ├── train.py
│ └── utils
│ ├── color.csv
│ ├── for_review.py
│ ├── __init__.py
│ ├── load.py
│ ├── matching.py
├── Discriminator
│ ├── Dataaugmentation.py
│ ├── distribution_sigmoid.py
│ ├── entropy_image_level.py
│ ├── eval.py
│ ├── __init__.py
│ ├── load.py
│ ├── predict.py
│ ├── resnet_dropout.py
│ ├── train.py
│ └── utils.py
├── main.py
├── Model
│ ├── Detection
│ │ └── step0
│ └── Discriminator
│ └── step0
If you find the code useful for your research, please cite:
@inproceedings{cho2021cell,
title={Cell detection in domain shift problem using pseudo-cell-position heatmap},
author={Cho, Hyeonwoo and Nishimura, Kazuya and Watanabe, Kazuhide and Bise, Ryoma},
booktitle={Medical Image Computing and Computer Assisted Intervention--MICCAI 2021: 24th International Conference, Strasbourg, France, September 27--October 1, 2021, Proceedings, Part VIII 24},
pages={384--394},
year={2021},
organization={Springer}
}