Hey everyone,
Just wanted to share (SeBRe-Segmenting Brain Regions) a tool that I have developed recently to register an atlas/segment brain regions in analysing large scale mouse/human brain images. All the testing is done on Allen brain mouse imaging (ISH/FISH) datasets.
Paper: https://rdcu.be/bGefW
Code: https://github.com/itsasimiqbal/SeBRe
Hope you all find it useful for your purpose. Please reach out to me if there’s any trouble in running the code. Thanks! 
Best,
Asim