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

Stitching Tiles

This page will walk you through how to stitch tiles already downloaded  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 

We will do with in a Jupyter Notebook.   There are two ways to open a notebook we will provide directions using anaconda but you can do this on the command line by following the directions in jupyter


Open Anaconda

If you need to click install and folow directions otherwise, Launch jupyter notebook

A jupyter notebook should open in your browser



Open a new juptyer notebook using python 3

Copy the script

You can get the script by downloading it from here

Specific Tutorial on getting the code from Github is provided here  (Note: use the script)

Choose Run 

Add a New Cell 

 Adjust KidneyRGBSticher to match your project

Target_dir is  directory where your tiles are this should be surrounded by single ‘

out_dir is the director where to put the stitched files should be surrounded by single ‘

down_sample = a number of downsampling to match the classifier you are using 

Interval = matches size you are using 

Tile_size is the tile size that matches the classifier 

Choose Run

Stitched files .png should be in output directory for each slide