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

Converting Raw Scores to Age Scores

This page will walk you through how to take the raw output of the aging classisier and convert it to a complied Age score.    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 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

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 CombinedAgescore to match your project

CombinedAgeScore(“RawScore_directory”, “AgeScore_directory”, image_dir=”StitchedTiles_Directory”, thresh_meathod=”GaussianBlur”, thresh_param=200,
dist=scipy.stats.norm, loc=0, scale=1)

RawScore_directory is  directory where your output from running the classifer should be surrounded by doube “

AgeScore_directory is the director where to put the combined age scores  should be surrounded by double “

image_dir = is directory  where your stiched tiles from before the classier are this should be surrounded by double “

If you are using our classifieres, the other parameters likey do not need to be adjusted

thresh_meathod=”GaussianBlur”. Otsu and Percentile are other options




Choose Run

Complied Age scores should now be in directory and .zarr files