Geropathology Imaging - Part of the The Jackson Laboratory Shock Center of Excellence in the Basic Biology of Aging
Using our classifier uses 4 different pieces of software, all of them free.
While strictly not required, we group Omero in the required list because we highly recommend that you store your images here. It is a great way to store images with metadata , share them and visualize them. There are great tools that will allow more and more image analysis options straight off the original Images stored in Omero so the original is safe but downstream processing is easy. https://www.openmicroscopy.org/omero/
As we are using software that others have written we will write specific directions and tutorials of all of the specific part of each piece of software we use but in many cases these tools can do more than we will highlight and often their developers have excellent tutorials and manuals we will try to directly link to.https://www.openmicroscopy.org/training/
Qupath is one of the pieces of image analysis tools that will read right from Omero. Qupath is an important tool for annotation and segmentation. Depending on how your slides are made they likely have at minimum lots of space that does not have tissue that is captured by a whole slide scanner there might be multiple sections on a slide etc. Qupath lets you build a way to easily segment parts of tissues and index locations https://qupath.github.io/
The Qupath tutorials can be found here Qupath Manuals and if you prefer via video Qupath Video Tutorials
This is the piece of software that will likely be the most intimidating for novice coders. Julia is a coding language that has the tools built in to allow us to train the computer to recognize the “patterns” of aging. https://julialang.org/.
If you are brand new to coding we have found that this tutorial to be a really good place to start Julia coding Basics If you want specifc Julia documentation the manual can be found here Julia Manual
Jupyter notebook is a flexible web-based environment that we use to visualize results and do statistics. If you are familiar with coding you can install directly from juptyer.org, however, if you would prefer to limit your coding you can install anaconda https://www.anaconda.com/and access jupyter that way.
Documentation for Jupyter notebook can be found at here Jupyter manual
Installing software on computers often involves permissions and possibly involves different rules for different institutions. This is not our area of expertise but we can try to be of help if you get stuck so please ask (Link to Contact US Form)