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cov19

https://github.com/lisatwyw/cov19

Science Score: 44.0%

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    Found CITATION.cff file
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    Low similarity (6.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: lisatwyw
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 95.7 KB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Created over 3 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation

README.md

Classification of disease severity using the COV19-CT-DS

COV19-CT-DB

Data folders and file counts

Summary:

|Diagnosis| Subset| n | Count per severity class | |:--|:--|:--|:--| |noncovid| train | | N/A | | | val | | N/A | | | test | | N/A | |covid| train | 460 | 132, 123, 166, 39 | | | val | 101 | 31, 20, 45, 5 | | | test | 231 | N/A |

Reproducing results

  1. Installation pip install -r requirements.txt

2a. Run interactively in ipython or python ``` $ ipython

In [1]: BS=128; IMGSET='all2'; MID='wideres101'; exec( open('icassp_sep.py').read() ) ```

2b. Run non-interactively ``` $ python icassp_sep.py 1 0 16

MID=1

FT=0 # FT=0 : Fine tune the last layer only

# FT=1 : Fine tune all layers

BS=16

```

Thank you for your exploration of this repo and consideration to cite this work: Tang LY. Severity classification of ground-glass opacity via 2-D convolutional neural network and lung CT scans: a 3-day exploration. arXiv preprint arXiv:2303.16904. 2023 Mar 23.

@article{tang2023severity, title={Severity classification of ground-glass opacity via 2-D convolutional neural network and lung CT scans: a 3-day exploration}, author={Tang, Lisa YW}, journal={arXiv preprint arXiv:2303.16904}, year={2023} }

Other resources

Datasets

  • https://www.eibir.org/covid-19-imaging-datasets/
  • https://www.kaggle.com/code/utkarshsaxenadn/ct-scans-3d-data-3d-data-processing-3d-cnn#3D-Scans-Data-Loading

Lung mask segmentation code

https://github.com/pzaffino/COVID19-intensity-labeling/blob/main/lungs_processing.py
- uses Simple ITK

Owner

  • Login: lisatwyw
  • Kind: user

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Tang"
  given-names: "Lisa Y.W."
  orcid: "https://orcid.org/0000-0003-2545-8440"
title: "cov19"
version: 1.0.0
doi: 
date-released: 2024-05-22
url: "https://github.com/lisatwyw/cov19"

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