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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  1. Fundamentals

Getting Set Up

These are the mandatory Prerequisites you would need to run the Analysis on QuPath and on your laptop!

PreviousSimple PipelineNextQuPath H-DAB Tutorial

Last updated 9 months ago

To open your slide scanned files, to just have a look at them there are different software depending on the company of the slides scanner:

  • 3D HISTECH Ltd - .mrsx files -

  • Hamamatsu - .ndpi files -

  • Zeiss - .czi files -

  • Venata - .bfi files -

The docs will in detail explain how to install everything.

Prerequsites for QuPath

The open software for image analysis QuPath is required to perfrom the analysis leading to the immunopositivity rate.

  • 0.4.3 or higher

Additional information on image analysis with QuPath can be found .

Prerequisites for Result Analysis

To process the data coming out of the previous QuPath step, to use this analysis, you should have installed in your laptop:

  • : pandas, numpy, seaborn and matplotlib

  • Pip library openpyxl > 3.2.0

If your not familiar with Python or how to install packages, please refer to this and to the non-expert page.

🛠️
CaseViewer
NDP.view2
ZEISS ZEN lite
non-expert
QuPath
here
Git
as an interface
Python 3.7 or higher
Required Python packages
link