This project was made with a focus on contrast stretching of blockface images, stacking and registration. With the code you are able to:
- Convert images from RAW to png and with a resize of 25 %
- Semi manual cropping of the images
- Segmentation of the brain with either converting the images to CMYK and performing an Otsu on the mergenta channel or performing an Otsu on the original PNG image
- Simple alignment with translation
- Contrast enhancement with the method CLAHE together with a sharpening of the images
- Stacking of the images with defined dimensions and creation of nifti files
- Rigid, Affine and SyN registraion with options to change parameters
To run the project, simply run CMenu in MATLAB.
The code use several external software, so for it to be able to run following software need to be installed:
- MATLAB 2015 or older with image processing toolbox. Problems with MATLAB 2016 has been experienced so we recommend using older versions.
- Advanced Normalization Tools (ANTs) by stnava. Can be found here: http://stnava.github.io/ANTs/
- ImageMagick. Can be found here: http://www.imagemagick.org/script/binary-releases.php
- Tools for NIfTI and ANALYZE image. Can be found here: https://se.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
- MINC toolkit version 1.9.11. Can be found here: https://bic-mni.github.io/#v2-version-19111911
- Catharina Maria Hamer Holland - [email protected]
- Christoffer Gøthgen - [email protected]
- Christos Zoupis Schoinas - [email protected]
- Andrew Janke - [email protected]