🛠️Getting Set Up

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

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 - CaseViewer

• Hamamatsu - .ndpi files - NDP.view2

• Zeiss - .czi files - ZEISS ZEN lite

• Venata - .bfi files -

The non-expert 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.

• QuPath 0.4.3 or higher

Additional information on image analysis with QuPath can be found here.

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:

• Git as an interface

• Python 3.7 or higher

• Required Python packages: 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 link and to the non-expert page.