QuPath H-DAB Project
  • 📊QuPath guide for H-DAB Cell Counting Docs
  • 💡Pipeline
    • 💡Simple Pipeline
  • Fundamentals
    • 🛠️Getting Set Up
  • QuPath H-Dab Docs
    • 💡QuPath H-DAB Tutorial
      • Creating and Opening of Projects
      • Estimating Stain Vectors
      • Training Image Creation
      • Cell Detection
      • Object Classifier
      • Tissue Detection
        • 1️⃣Automatic General Tissue Detection
        • 2️⃣Manual Specific Tissue Detection
    • 🧾QuPath Script
      • Batch Processing
    • 📂Output
  • Result Analysis Docs
    • 💡Processing Package Tutorial
      • Addition Information for Python insiders
      • In-Depth Python usage
    • 🗄️Final Spreadsheet creation
    • 🆘Out-of-memory error
  • non-expert docs
    • 🔎QuPath Installation
    • 💻Git Bash Installation
    • 🖥️Python Installation & Packages
    • Git Bash installation
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Batch Processing

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Last updated 11 months ago

  1. Once the stain vectors and the cell detection have been replaced in the script, the script can be run on the slides. To test whether everything is right, as a test the script should be run on a single slide by just clicking on Run.

  2. By clicking on the three little dots next to run "Run for project" can be selected.

  3. The HDAB_BatchProcessing Script automatically generates a Results folder containing .txt files.

This might take a while and the capacity for your laptop to run the script on all the slides. Other programs on your laptop might run slower.

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Batch Porcessing with script