ndreg is a Python package that performs non-linear affine and deformable image registration.
A joint project between Neurodata and Karl Deisseroth’s Lab. This project aims to create software tools to analyze CLARITY brain imaging data including tools for image preprocessing, registration, cell body detection, and fiber tracking.
R. Burns et al. A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data. Nature Methods, 2018.
K. S. Kutten et al. A Large Deformation Diffeomorphic Approach to Registration of CLARITY Images via Mutual Information. International Conference on Medical Image Computing and Computer-Assisted Intervention, 2017.
K. S. Kutten et al. Deformably Registering and Annotating Whole CLARITY Brains to an Atlas via Masked LDDMM. SPIE Europe, 2016.
L. Ye et al. Wiring and molecular features of prefrontal ensembles representing distinct experiences. Cell, 2016.
K. Chung and K. Deisseroth. CLARITY for mapping the nervous system. Nature methods, 2013.
K. Chung et al. Structural and molecular interrogation of intact biological systems. Nature, 2013.