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CheXpert Chest X-Ray Classification

Name: Potato
Author: Potato

Multi-label classification of chest radiographs for 14 observations (Irvin et al., AAAI 2019). Annotate chest X-rays with pathology labels including uncertainty handling for clinical findings.

Configuration Fileconfig.yaml

This Potato config reproduces the annotation task. Save it as config.yaml and run potato start config.yaml to try it.

yaml

# CheXpert Chest X-Ray Classification Configuration
# Based on Irvin et al., AAAI 2019

annotation_task_name: "CheXpert Chest X-Ray Classification"
task_dir: "."

data_files:
  - "sample-data.json"

item_properties:
  id_key: "id"
  text_key: "image_url"
  context_key: "context"

user_config:
  allow_all_users: true

annotation_schemes:
  - annotation_type: "radio"
    name: "cardiomegaly"
    description: "Cardiomegaly (enlarged heart)"
    labels:
      - name: "positive"
        tooltip: "Finding is present"
      - name: "negative"
        tooltip: "Finding is absent"
      - name: "uncertain"
        tooltip: "Cannot determine with certainty"
      - name: "not_mentioned"
        tooltip: "Not applicable or not assessed"

  - annotation_type: "radio"
    name: "edema"
    description: "Pulmonary edema"
    labels:
      - name: "positive"
      - name: "negative"
      - name: "uncertain"
      - name: "not_mentioned"

  - annotation_type: "radio"
    name: "consolidation"
    description: "Lung consolidation"
    labels:
      - name: "positive"
      - name: "negative"
      - name: "uncertain"
      - name: "not_mentioned"

  - annotation_type: "radio"
    name: "atelectasis"
    description: "Atelectasis (lung collapse)"
    labels:
      - name: "positive"
      - name: "negative"
      - name: "uncertain"
      - name: "not_mentioned"

  - annotation_type: "radio"
    name: "pleural_effusion"
    description: "Pleural effusion (fluid around lungs)"
    labels:
      - name: "positive"
      - name: "negative"
      - name: "uncertain"
      - name: "not_mentioned"

  - annotation_type: "radio"
    name: "pneumonia"
    description: "Pneumonia"
    labels:
      - name: "positive"
      - name: "negative"
      - name: "uncertain"
      - name: "not_mentioned"

  - annotation_type: "radio"
    name: "pneumothorax"
    description: "Pneumothorax (collapsed lung)"
    labels:
      - name: "positive"
      - name: "negative"
      - name: "uncertain"
      - name: "not_mentioned"

  - annotation_type: "radio"
    name: "no_finding"
    description: "No significant findings"
    labels:
      - name: "positive"
        tooltip: "Normal study, no findings"
      - name: "negative"
        tooltip: "Abnormalities present"

  - annotation_type: "radio"
    name: "image_quality"
    description: "Rate the image quality"
    labels:
      - name: "diagnostic"
        tooltip: "Adequate for diagnosis"
      - name: "suboptimal"
        tooltip: "Limited but usable"
      - name: "non_diagnostic"
        tooltip: "Inadequate for diagnosis"

interface_config:
  item_display_format: "<img src='{{text}}' style='max-width:100%; max-height:500px; background:#000;'/><br/><small>{{context}}</small>"

output_annotation_format: "json"
output_annotation_dir: "annotations"

Sample Datasample-data.json

json

[
  {
    "id": "cxr_001",
    "image_url": "https://upload.wikimedia.org/wikipedia/commons/c/c5/Normal_posteroanterior_%28PA%29_chest_radiograph_%28X-ray%29.jpg",
    "context": "Chest X-ray PA view. Assess for cardiomegaly, edema, consolidation, atelectasis, pleural effusion, pneumonia, and pneumothorax."
  },
  {
    "id": "cxr_002",
    "image_url": "https://upload.wikimedia.org/wikipedia/commons/2/29/Chest_X-ray_of_RTI.jpg",
    "context": "Chest radiograph. Label all visible pathological findings. Use 'uncertain' when findings are equivocal."
  }
]

// ... and 1 more items

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Get This Design

View on GitHub

Clone or download from the repository

Quick start:

git clone https://github.com/davidjurgens/potato-showcase.git
cd potato-showcase/image/medical/chexpert
potato start config.yaml

Dataset & paper

Irvin et al., AAAI 2019

Official dataset ↗Read the paper ↗

Citation (BibTeX)

bibtex

@inproceedings{irvin2019chexpert,
    title = "{CheXpert}: A Large Chest Radiograph Dataset with Uncertainty Labels and Expert Comparison",
    author = "Irvin, Jeremy  and Rajpurkar, Pranav  and Ko, Michael  and Yu, Yifan  and Ciurea-Ilcus, Silviana  and Chute, Chris  and Marklund, Henrik  and Haghgoo, Behzad  and Ball, Robyn  and Shpanskaya, Katie  and others",
    booktitle = "Proceedings of the AAAI Conference on Artificial Intelligence",
    volume = "33",
    pages = "590--597",
    year = "2019",
    url = "https://ojs.aaai.org/index.php/AAAI/article/view/3834"
}

Details

Annotation Types

radio

Domain

Medical ImagingRadiology

Use Cases

Chest X-Ray ClassificationMedical DiagnosisClinical AI

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