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Updated readme
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Christoffer Edlund committed May 7, 2021
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1 change: 0 additions & 1 deletion README.md
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Expand Up @@ -199,7 +199,6 @@ nuclear_count_benchmark/
├── A549.zip
├── A549_counts.json
└── A549_fluorescent_images.zip
```

The json files are on the following format:
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30 changes: 25 additions & 5 deletions model/README.md
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Expand Up @@ -5,11 +5,31 @@ based on the [detectron2-ResNeSt](https://github.com/chongruo/detectron2-ResNeSt
which is both built upon the [detectron2](https://github.com/facebookresearch/detectron2) library.

The models trained for the LIVECell paper was done so in a distributed fashion on 8 Nvidia V100 GPUS.
To help others reproduce our results, the training is fully specified in config files found under TODO: (provide real links)
````
LIVECell/model/anchor_free/[config_name].yaml
LIVECell/model/anchor_based/[config_name].yaml
````
To help others reproduce our results, we provide pre-trained models and config files.


| Architecture | Dataset | box AP | mask AP | download
| ------------ | : ------ : | : ---- : | :----:| :-----: |
| Anchor_free | LIVECell | 48.45 | 47.78 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_free/livecell_config.yaml) / [model]() |
| | A172 | 31.49 | 34.57 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_free/a172_config.yaml) / [model]() |
| | BT-474 | 42.12 | 42.60 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_free/bt474_config.yaml) / [model]() |
| | BV-2 | 42.62 | 45.69 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_free/bv2_config.yaml) / [model]() |
| | Huh7 | 42.44 | 45.85 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_free/huh7_config.yaml) / [model]() |
| | MCF7 | 36.53 | 37.30 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_free/mcf7_config.yaml) / [model]() |
| | SH-SY5Y | 25.20 | 23.91 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_free/shsy5y_config.yaml) / [model]() |
| | SkBr3 | 64.35 | 65.85 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_free/skbr3_config.yaml) / [model]() |
| | SK-OV-3 | 46.43 | 49.39 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_free/livecell_config.yaml) / [model]() |
| Anchor_based | LIVECell | 48.43 | 47.89 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_based/livecell_config.yaml) / [model]() |
| | A172 | 36.37 | 38.02 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_based/a172_config.yaml) / [model]() |
| | BT-474 | 43.25 | 43.00 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_based/bt474_config.yaml) / [model]() |
| | BV-2 | 54.36 | 52.60 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_based/bv2_config.yaml) / [model]() |
| | Huh7 | 52.79 | 51.83 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_based/huh7_config.yaml) / [model]() |
| | MCF7 | 37.53 | 37.94 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_based/mcf7_config.yaml) / [model]() |
| | SH-SY5Y | 27.87 | 24.92 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_based/shsy5y_config.yaml) / [model]() |
| | SkBr3 | 64.41 | 65.39 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_based/skbr3_config.yaml) / [model]() |
| | SK-OV-3 | 53.29 | 54.12 | [config](https://github.com/sartorius-research/LIVECell/blob/main/model/anchor_based/skov3_config.yaml) / [model]() |



To use our fully trained models download them from our S3 bucket, and use it togheter with appropriate config file as
described below in the [traing and evaluation section](#Training and evaluation)
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