Camelyon17 - Breast Cancer Metastasis Detection in Pathology

# Camelyon17 - Breast Cancer Metastasis Detection in Pathology
# Based on Ehteshami Bejnordi et al., JAMA 2017
# Paper: https://jamanetwork.com/journals/jama/fullarticle/2665774
# Dataset: https://camelyon17.grand-challenge.org/
#
# Pathology whole-slide image annotation for detecting breast cancer metastases
# in sentinel lymph node tissue. Annotators outline tumor regions using polygon
# and bounding box tools, then classify the overall slide-level diagnosis.
#
# Region Labels:
# - Tumor Region: Areas containing metastatic cancer cells
# - Normal Tissue: Healthy lymph node tissue
# - Artifact: Tissue folding, bubbles, or staining artifacts
# - Background: Non-tissue areas (glass, mounting medium)
#
# Annotation Guidelines:
# 1. Examine the histopathology image at available magnification
# 2. Use polygon tool for precise tumor boundary delineation
# 3. Use bounding box for quick region-of-interest marking
# 4. Classify the slide as positive, negative, or uncertain for metastasis
# 5. Tumor cells appear as dense, darkly stained clusters with irregular nuclei

annotation_task_name: "Camelyon17 - Pathology Metastasis Detection"
task_dir: "."

data_files:
  - sample-data.json

item_properties:
  id_key: "id"
  text_key: "text"

output_annotation_dir: "annotation_output/"
output_annotation_format: "json"

port: 8000
server_name: localhost

annotation_schemes:
  # Step 1: Annotate regions in the pathology image
  - annotation_type: image_annotation
    name: tissue_regions
    description: "Delineate tissue regions in the pathology slide. Use polygon for precise boundaries, bounding box for quick marking."
    tools:
      - polygon
      - bbox
    labels:
      - "Tumor Region"
      - "Normal Tissue"
      - "Artifact"
      - "Background"

  # Step 2: Slide-level classification
  - annotation_type: radio
    name: slide_diagnosis
    description: "What is the overall slide-level diagnosis for metastasis?"
    labels:
      - "Positive (Metastasis Present)"
      - "Negative (No Metastasis)"
      - "Uncertain"
    keyboard_shortcuts:
      "Positive (Metastasis Present)": "1"
      "Negative (No Metastasis)": "2"
      "Uncertain": "3"
    tooltips:
      "Positive (Metastasis Present)": "One or more tumor regions are clearly identifiable in the slide"
      "Negative (No Metastasis)": "No tumor cells are visible; the tissue appears entirely normal"
      "Uncertain": "Suspicious regions are present but a definitive diagnosis cannot be made"

annotation_instructions: |
  You will annotate histopathology images of sentinel lymph node tissue sections
  for the presence of breast cancer metastases.

  For each slide:
  1. Examine the tissue section carefully at available magnification.
  2. Use the polygon tool to precisely outline any tumor regions you identify.
     - Tumor cells typically appear as dense clusters with large, irregular,
       darkly stained nuclei.
     - Metastases may appear as isolated tumor cells (ITC), micrometastases,
       or macrometastases.
  3. Use the bounding box tool for quick marking of suspicious areas.
  4. Label non-tumor regions as Normal Tissue, Artifact, or Background.
  5. Provide an overall slide-level diagnosis.

  Important:
  - Artifacts (tissue folds, air bubbles, poor staining) should not be confused with tumor.
  - When uncertain, mark as Uncertain and outline the suspicious region.
  - This task requires familiarity with histopathology.

html_layout: |
  <div style="padding: 15px; max-width: 900px; margin: auto;">
    <div style="display: flex; gap: 12px; margin-bottom: 14px; flex-wrap: wrap;">
      <div style="background: #fce4ec; padding: 7px 14px; border-radius: 8px;">
        <strong>Tissue Type:</strong> {{tissue_type}}
      </div>
    </div>
    <div style="text-align: center; margin-bottom: 16px; background: #212121; padding: 12px; border-radius: 8px;">
      <img src="{{image_url}}" style="max-width: 100%; max-height: 600px; border-radius: 4px;" alt="Histopathology slide" />
    </div>
    <div style="background: #f0f9ff; border: 1px solid #bae6fd; border-radius: 8px; padding: 16px; margin-bottom: 16px;">
      <strong style="color: #0369a1;">Slide Description:</strong>
      <p style="font-size: 15px; line-height: 1.7; margin: 8px 0 0 0;">{{text}}</p>
    </div>
  </div>

allow_all_users: true
instances_per_annotator: 30
annotation_per_instance: 3
allow_skip: true
skip_reason_required: false