pipeline_image_processing.m : creates 3D nifti stacks from Tissuecyte sections and maps them to the Allen template pipeline_map_points.m : maps detected cells to the Allen template pipeline_mip.m : create nice images
depends on matlab nifti tools https://www.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image