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.



Performs non-linear affine and deformable image registration.


The deployment of tools which support the Open Connectome Project


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. Society of Photo-Optical Instrumentation Engineers Europe, 2016.

K. Chung and K. Deisseroth. CLARITY for mapping the nervous system. Nature methods, 2013.

People on project

Vikram Chandrashekhar
Ailey Crow
Joshua Vogelstein
Karl Deisseroth


NeuroNex Technology Hub: Integrated Circuit Cracking (ICC) with Linked Tools for Diverse Systems