Geropathology Imaging - Part of the The Jackson Laboratory Shock Center of Excellence in the Basic Biology of Aging

Exporting Tiles from Qupath

This page will walk you through downloading tiles from qupath.  If you have not installed these programs you can get directions to do that here Required Software there are also links to the manuals and tutorials that both groups provide.  We also have links for how you can get Images from Omero to Qupath and Annotate slides in Qupath

Open QuPath Project

Open QuPath


Start Script Editor



Load Base Tile Export Script

You can get the script by downloading it from here

Specific Tutorial on getting the code from Github is provided here

Edit Script for your project

Make sure the labels match your project 

Adjust tilesize and overlap to match the classifer you are using 

Kidney: Tile Size = 512, Overlap =0

Choose Run 

Select Run for Project

Select Images you want to run 

Move Image to the right pannel

Tiles can now be viewed in project folder