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MIMIC-CXR Chest Radiograph Classification

Large-scale chest radiograph classification based on MIMIC-CXR (Johnson et al., Scientific Data 2019). Multi-label classification with 14 observations derived from radiology reports.

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Quick start:

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

Configuration File

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

yaml
# MIMIC-CXR Chest Radiograph Classification Configuration
# Based on Johnson et al., Scientific Data 2019

annotation_task_name: "MIMIC-CXR Chest Radiograph Classification"
task_dir: "."

data_files:
  - "sample-data.json"

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

user_config:
  allow_all_users: true

annotation_schemes:
  - annotation_type: "multiselect"
    name: "findings"
    description: "Select all findings present in the image"
    labels:
      - name: "atelectasis"
        tooltip: "Partial or complete lung collapse"
      - name: "cardiomegaly"
        tooltip: "Enlarged heart"
      - name: "consolidation"
        tooltip: "Lung tissue filled with fluid"
      - name: "edema"
        tooltip: "Pulmonary edema"
      - name: "enlarged_cardiomediastinum"
        tooltip: "Enlarged heart and mediastinum"
      - name: "fracture"
        tooltip: "Bone fracture visible"
      - name: "lung_lesion"
        tooltip: "Mass or nodule"
      - name: "lung_opacity"
        tooltip: "Abnormal opacity"
      - name: "pleural_effusion"
        tooltip: "Fluid in pleural space"
      - name: "pleural_other"
        tooltip: "Other pleural abnormality"
      - name: "pneumonia"
        tooltip: "Pneumonia"
      - name: "pneumothorax"
        tooltip: "Air in pleural space"
      - name: "support_devices"
        tooltip: "Medical devices present"

  - annotation_type: "radio"
    name: "no_finding"
    description: "Is this a normal study?"
    labels:
      - name: "normal"
        tooltip: "No significant findings"
      - name: "abnormal"
        tooltip: "Abnormalities present"

  - annotation_type: "radio"
    name: "view_position"
    description: "What is the view position?"
    labels:
      - name: "PA"
        tooltip: "Posteroanterior"
      - name: "AP"
        tooltip: "Anteroposterior"
      - name: "lateral"
        tooltip: "Lateral view"

  - annotation_type: "text"
    name: "additional_notes"
    description: "Additional clinical notes or observations"

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

output_annotation_format: "json"
output_annotation_dir: "annotations"

Sample Data

json
[
  {
    "id": "mimic_001",
    "image_url": "https://upload.wikimedia.org/wikipedia/commons/a/a1/Normal_posteroanterior_%28PA%29_chest_radiograph_%28X-ray%29.jpg",
    "report_excerpt": "PA and lateral views of the chest. Heart size normal. Lungs are clear."
  },
  {
    "id": "mimic_002",
    "image_url": "https://upload.wikimedia.org/wikipedia/commons/5/51/X-ray_of_lobar_pneumonia.jpg",
    "report_excerpt": "Frontal chest radiograph. Evaluate for cardiopulmonary disease."
  }
]

// ... and 1 more items

Dataset & paper

Johnson et al., Scientific Data 2019

Official dataset(opens in a new tab)Read the paper(opens in a new tab)

Citation (BibTeX)

bibtex
@article{johnson2019mimic,
    title = "{MIMIC-CXR}, a de-identified publicly available database of chest radiographs with free-text reports",
    author = "Johnson, Alistair E. W.  and Pollard, Tom J.  and Berkowitz, Seth J.  and Greenbaum, Nathaniel R.  and Lungren, Matthew P.  and Deng, Chih-ying  and Mark, Roger G.  and Horng, Steven",
    journal = "Scientific Data",
    volume = "6",
    number = "1",
    pages = "317",
    year = "2019",
    publisher = "Nature Publishing Group",
    doi = "10.1038/s41597-019-0322-0",
    url = "https://www.nature.com/articles/s41597-019-0322-0"
}

Details

Annotation Types

multiselectradiotext

Domain

Medical ImagingRadiology

Use Cases

Chest X-Ray ClassificationRadiology AIClinical Documentation

Tags

mimicmedicalchest-xrayradiologyphysionethealthcare

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