Creating and Opening of Projects

Easiest way to start a batch analysis is to start a project on QuPath, specific for each antibody.

After opening QuPath, these are the steps to follow:

1. Create project › Select empty folder (e.g IL-1)

1. Add images (to the new Created project) ›

   • Image provider -> default

   • Set image type -> H-DAB

   • Choose files -> Select slide scans from specific stain (e.g. IL1)

This might take a while depending on how many images you are importing and on the processor of your laptop.

1. Create two projects containing identical slides; one to perform all the training on (xx_Calssifiers); and the other for running the final analysis within the specific regions. (xx_Regions). The first part of this guide will be performed in the Classifiers project, the final analysis will be performed in the Regions project. It is clearly stated when to switch and what to copy from the Classifiers to the Regions project folder.

Folder system to perform the analysis

1. Open project › Select “project.qpproj” in IL1

   (This file is automatically generated in Step 1)

1. Now open up the _Classifier project