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The purpose of the tools found in this repository is to provide a way to sample cortical laminae in 2D images (Histology) by creating a coordinate system for individual slides.
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Provide a tool that allows alignment of 1D profiles across multiple subjects and slides, to a common reference, obtained from coordinate system - this helps reduce the inherent anatomical variability from one are of the cortex from another.
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Develop unsupervised tools that help classify abnormal tissue found within the cortex using anomoly detection. ( In Development )
This code was developed to create a tool for sampling the laminae of the cortex in histology. Must clone the following git repository: https://github.com/jordandekraker/HippUnfolding. Add path to all subfolders. The repositroy contains laplace solver and few other tools used in the script
To run the call the function StreamLineComp(SegmentedImageDir,OutputDir). Assumes that you've inputed a segmented nifti image and that its in the directory you've specified. Segmented image contains 3 componets GM == 1, WM == 2, Background ==3, addtionally an ignore label ignore==4 which specifies regions to ignore. The ignore label is required and must be placed at the end of the tissue - an example is shown in the image below.
The function takes in two parameters:
- Input directory (Mandatory)
- Output directory (Default is current directory)
Resulting coordinate system overlaped ontop of Neuron Density Feature Map is shown below:
Read Coordinate System for the Cortical Laminae for more information about motivations and methods for the StreamLineComp script.