Geropathology Imaging - Part of the The Jackson Laboratory Shock Center of Excellence in the Basic Biology of Aging
How to use Aging Classifiers
We provide directions on how to make your own at the end
Concepts
Machine learning concepts can be difficult to understand. No programming or machine learning experience is necessary to use our tools, but some useful background information can be found here.
Link to basic concepts video
Link to Flow chart of work
Overall Workflow
The chart here overall shows you how to get from Images to Aging scores. We downsample the slides using Qupath then we use our classifers with Julia to extract Zarrs from the tiles then we use these files in the classifer to put and age score we then move to a Jupyter notebook to get data and do some statistics
Coding Basics
We want to support all levels of users. Coding was new to us when we started this process and understand that it can be intimidating. We hope that these recourses will provide confidence to new users.
Link to coding basicis
Links to Required Software
Required Software
There are 4 different pieces of software we utalize to go from Images to aging scores. The good news is that all of these are free! Follow the link to get to thier websites and installation directions
How to use our classifier:
While there are several ways to get to the downsampled tiles, we extract them from QuPath. QuPath is easy to use and interactive. We provide instructions on how to get to these tiles, assuming you’re storing images in Omero.
- You will need to get images from your Omero server into QuPath: Omero to QuPath.
- Once you have your Images in QuPath you will need to annotate them: Annotate Slides in QuPath.
- After the images are annotated you can use QuPath to export downsampled tiles: Exporting Tiles From QuPath.
- The tiles then need to be stitched together with a code declared in a Jupyter notebook: Stitching Tiles.
- After the images are stitched, you will then run them through a classifier: Run a Classifier.
- Once the classifier has been run you need to compile the raw age scores: Raw Age Scores to Compiled Age Scores.
- With the tissue scores in hand you can now visualize the results: Visualizing the Aged Classifier Results.
- The results can also be complied into a csv file for statistics: LINK
- We provide some statistics and graphs we think might be helpful for many users in R: LINK