Geometry Processing of Conventionally Produced Mouse Brain Slices.

Journal of Neuroscience Methods 2018 [Paper] [Project Page]

This is the code to register mouse brain microscopic images with annotated ARA atlas images. The method extracts dominant edges from both input images and aligns them using non-linear transformation. For more details please read the paper.

Getting Started

To run the demo, download the sample data

bash download_dataset.sh

Compile mex files

mex solveLaplace.cpp

Please read the run_me.m file.

Citation

If you use the code/data, please cite the following paper:

@article{agarwal2017mouse,
  author = {Nitin Agarwal, Xiangmin Xu, Gopi Meenakshisundaram},
  title = {Geometry Processing of Conventionally Produced Mouse Brain Slice Images},
  journal = {Journal of Neuroscience Methods},
  year = {2018}
}

License

Our code is released under MIT License (see License file for details).

Contact

Please contact Nitin Agarwal if you have any questions or comments.