The Inflammation Index packages (both in R and ImageJ) are no longer being actively supported - I've moved out of academia and no longer have the time outside of work to maintain these packages or give them the changes they need. If you're interested in working together to improve and interate on these packages, please get in touch via the discussions section.
In this repo you'll find all the code necessary to process 3D image stacks of microglia, extract morphological features for detected cells, and combine these features into a single metric of morphological change sensitive to the training data you provide. This is detailed in other READMEs in this repo, and also in the associated publication
You can follow progress on changes and updates to this GitHub repo and the R and Fiji plugins here and observe development of the Fiji plugin here
If you're having issues with the plugin that we are unable to resolve, you can find a standalone Fiji package here that you can download, update with the latest version of the plugin, and use to unblock your work. We have found that sometimes the plugin doesn't work with particular Fiji environments.
This file describes how to use the ImageJ plugin for image processing, cell detection, and morphological feature extraction.
This file describes how to use and install the Inflammation-Index R package to read in data extracted by the Microglia Morphology Analysis plugin, and use it to generate and apply an 'Inflammation Index' to novel data
Please post any questions, suggestions, etc. here
Outstanding issues, feature changes, updates etc. will be posted and tracked here
Contains the .jar and .py files necessary for running the Microglia Morphology Analysis ImageJ plugin. Drop the .jar file into your Fiji plugins folder, and the .py file into the plugins/scripts folder.
Contains the R package code that can be installed using devtools.
Contains images used to enrich the markdown README files.
Contains video files demonstrating how to use the Fiji plugin functions.