ANIMA (Analyzer for Neural Images by Matching Algorithm) is a Java-based image processing software specialized for immunohistochemically stained neuron images. This repository replaces thewindsofwinter/neural-analysis as a more permanent location for software storage as it is being developed.
The following paper utilizes ANIMA for analysis of neurodegeneration in brain images of mice.
Since its primary development in the summer of 2019, this Image Analysis Engine has been improved steadily. Unfortunately, documentation has not quite kept up with the improvements, which I seek to fix in the near-future. Please let me know (andyyt2@illinois.edu) if you have any trouble with the algorithm and I will work with you to resolve any issues.
Please note that the second section of the setup of the Image Analysis Engine is no longer necessary. I'll work on cleaning up instructions as well as writing cleaner code at some point in the future. There are also a variety of features that I wish to implement.
If there are any issues you find with this engine, please email andyyt2@illinois.edu and/or create an issue on this repository.
- Clean up code
- Menu to select which attributes to analyze
- Updated flood-fill algorithm to require more overlap
- Make the export-to-CSV option more robust
- Create an option to iterate through images
- Better set-up script + provide executable files
- Create web version (JS-ANIMA)
- Also create project website