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lingyigt authored Apr 29, 2024
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# PULSE Lab Repository Containing Simulated and Labeled In Vivo COVID-19 Dataset

Repository link: https://gitlab.com/pulselab/covid19

This external repository link provides public access to the datasets and code described in the paper “Detection of COVID-19 features in lung ultrasound images using deep neural networks.” Communications Medicine, 2024. https://www.nature.com/articles/s43856-024-00463-5.

Access includes 40,000 carefully simulated lung ultrasound B-mode images containing A-line, B-line, and consolidation features with paired ground truth segmentations. The simulation code can be accessed via the repository.

Access also includes segmentation annotations of the following publicly available POCUS datasets (available in https://github.com/jannisborn/covid19_ultrasound):

| File name | Source link | Feature | File name prefix in the data folder |
|----------------------------------------|------------------------------------------------------------------------------------------------------|---------------|-------------------------------------|
| Reg-Atlas-alines | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_034 |
| Reg_Avi_normal-A-lines-pleural-line | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_133 |
| Reg_Avi_lung-sliding | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_134 |
| Reg_Avi_lung-sliding-3 | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_135 |
| Reg_Avi_lung-sliding-2 | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_137 |
| Reg_Avi_normal-A-lines | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_139 |
| Reg_Avi_pleural-line-normal | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_151 |
| Reg_Avi_Image002 | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_157 |
| Reg_Avi_Image003 | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_159 |
| Reg_northumbria_0409_set3_vid1 | Data contributed by Northumbria Specialist Emergency Care Hospital | Aline | Reg_200 |
| Cov-Atlas-Day+2 | http://www.thepocusatlas.com/covid19 (Day2) | Bline | Cov_025 |
| Cov-Atlas-+(43) | http://www.thepocusatlas.com/covid19-1/ru6w5sgjyu1zn21jraypm2pfm0h6uf | Bline | Cov_030 |
| Cov-Atlas-suspectedCovid | http://www.thepocusatlas.com/covid19-1/lung-us-findings-in-hypoxic-patient-with-suspected-covid19 | Bline | Cov_036 |
| Cov_denault_proposedUS_vid1 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241588/ | Bline | Cov_293 |
| Cov_denault_proposedUS_vid2 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241588/ | Bline | Cov_294 |
| Cov_denault_proposedUS_vid13 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241588/ | Bline | Cov_299 |
| Cov_denault_proposedUS_vid14 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7241588/ | Bline | Cov_300 |
| Cov_combatting_Image1 | https://www.stemlynsblog.org/combatting-covid19-is-lung-ultrasound-an-option/ - third video | Bline | Cov_126 |
| Cov_combatting_Image2 | https://www.stemlynsblog.org/combatting-covid19-is-lung-ultrasound-an-option/ - fourth video | Bline | Cov_127 |
| Cov_combatting_Image3 | https://www.stemlynsblog.org/combatting-covid19-is-lung-ultrasound-an-option/ - fifth video | Bline | Cov_129 |
| Cov_combatting_image4 | https://www.stemlynsblog.org/combatting-covid19-is-lung-ultrasound-an-option/ - sixth video | Bline | Cov_130 |
| Cov_combatting_Image5 | https://www.stemlynsblog.org/combatting-covid19-is-lung-ultrasound-an-option/ - seventh video | Consolidation | Cov_131 |
| Reg_recommendations_alines_mov1 | https://theultrasoundjournal.springeropen.com/articles/10.1186/s13089-020-00177-4#author-information | Aline | Reg_255 |
| Cov_recommendations_likebutterfly_mov5 | https://theultrasoundjournal.springeropen.com/articles/10.1186/s13089-020-00177-4#author-information | Consolidation | Cov_259 |
| Cov_recommendations_lightbeam_mov6 | https://theultrasoundjournal.springeropen.com/articles/10.1186/s13089-020-00177-4#author-information | Bline | Cov_260 |
| Cov_convex_volpecelli_sonographic_v1 | https://theultrasoundjournal.springeropen.com/articles/10.1186/s13089-020-00171-w | Bline | Cov_288 |
| Cov_convex_volpecelli_sonographic_v2 | https://theultrasoundjournal.springeropen.com/articles/10.1186/s13089-020-00171-w | Bline | Cov_289 |
| Cov_convex_volpecelli_sonographic_v3 | https://theultrasoundjournal.springeropen.com/articles/10.1186/s13089-020-00171-w | Bline | Cov_290 |
| Cov_convex_volpecelli_sonographic_v4 | https://theultrasoundjournal.springeropen.com/articles/10.1186/s13089-020-00171-w | Bline | Cov_291 |
| Cov_convex_volpecelli_sonographic_v5 | https://theultrasoundjournal.springeropen.com/articles/10.1186/s13089-020-00171-w | Bline | Cov_292 |
| Cov_Oliviera_2020_Fig5A | https://www.scielo.br/img/revistas/rb/v53n4//0100-3984-rb-20200051-gf05.jpg | Bline | Cov_364 |
| Cov_Oliviera_2020_Fig15A | https://www.scielo.br/img/revistas/rb/v53n4//0100-3984-rb-20200051-gf15.jpg | Bline | Cov_366 |
| Cov_emdocs_vid1 | http://www.emdocs.net/wp-content/uploads/2020/04/R-apex-1.gif | Bline | Cov_373 |
| Cov_emdocs_vid3 | http://www.emdocs.net/wp-content/uploads/2020/04/unnamed.gif | Bline | Cov_375 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_003 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Aline | Reg_004 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_006 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_007 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_008 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Consolidation | Cov_009 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Consolidation | Cov_010 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Consolidation | Cov_011 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Consolidation | Cov_013 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_014 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_015 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_016 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_018 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_019 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_020 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_021 |
| Butterfly | https://www.butterflynetwork.com/covid19/covid-19-ultrasound-gallery | Bline | Cov_022 |

If you use the simulated datasets, labels, and/or code in this external repository, cite the following references:

1. L. Zhao, T.C. Fong, M.A.L. Bell, “Detection of COVID-19 features in lung ultrasound images using deep neural networks”, Communications Medicine, 2024. https://www.nature.com/articles/s43856-024-00463-5

```bib
@article{zhao2024detection,
title={Detection of COVID-19 features in lung ultrasound images using deep neural networks},
author={Zhao, Lingyi and Fong, Tiffany Clair and Bell, Muyinatu A Lediju},
journal={Communications Medicine},
volume={4},
number={1},
pages={41},
year={2024},
publisher={Nature Publishing Group UK London}
}
```

2. L. Zhao, M.A.L. Bell (2023). Code for the paper “Detection of COVID-19 features in lung ultrasound images using deep neural networks”. Zenodo. https://doi.org/10.5281/zenodo.10324042

```bib
@misc{zenodo,
title={Code for the paper “Detection of COVID-19 features in lung ultrasound images using deep neural networks"},
author={Zhao, Lingyi and Bell, Muyinatu A Lediju},
year={2024},
publisher={Zenodo}
url={https://doi.org/10.5281/zenodo.10324042}
}
```
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -10,7 +10,7 @@ This repo contains the code for the paper `Accelerating Detection of Lung Pathol
### Dataset
Feel free to use (and cite) our dataset. We currently have >200 LUS videos labelled with a diagnostic outcome. Moreover, lung severity scores for 136 videos are made available in the [dataset_metadata.csv](./data/dataset_metadata.csv) under the column **"Lung Severity Score"** from [Gare et al., 2022](https://arxiv.org/abs/2201.07357). Further clinical information (symptoms, visible LUS patterns etc) are provided for some videos. For details see [data/README.md](data/README.md).

If you are looking for more data, please consider using the 40,000 [carefully simulated LUS images](https://gitlab.com/pulselab/covid19) from the paper by [Zhao et al. (2024, *Communications Medicine*)](https://www.nature.com/articles/s43856-024-00463-5) that were partially derived from the data in this repo.
If you are looking for more data, please consider using the 40,000 [carefully simulated LUS images](https://gitlab.com/pulselab/covid19) and paired labels from the paper by [Zhao et al. (2024, *Communications Medicine*)](https://www.nature.com/articles/s43856-024-00463-5). In addition, segmentation labels for a subset of the in vivo data in this repo are also available. For details see [PULSE Lab Repository/README.md](PULSE%20Lab%20Repository/README.md).

**NOTE: Please make sure to create a meaningful train/test data split. Do not split the data on a frame-level, but on a video/patient-level. The task becomes trivial otherwise. See the instructions [here](pocovidnet/#cross-validation-splitting).**

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