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


J. T. Vogelstein, E. Perlman, B. Falk, A. Baden, W. Gray Roncal, V. Chandrashekhar, F. Collman, S. Seshamani, J. L. Patsolic, K. Lillaney, M. Kazhdan, R. Hider, D. Pryor, J. Matelsky, T. Gion, P. Manavalan, B. Wester, M. Chevillet, E. T. Trautman, K. Khairy, E. Bridgeford, D. M. Kleissas, D. J. Tward, A. K. Crow, B. Hsueh, M. A. Wright, M. I. Miller, S. J. Smith, R. J. Vogelstein, K. Deisseroth, and R. Burns. A Community-Developed Open-Source Computational Ecosystem for Big Neuro Data. Nature Methods, (11)15:846-847, 2018.

K. S. Kutten, N. Charon, M. I. Miller, J. T. Ratnanather, J. Matelsky, A. D. Baden, K. Lillaney, K. Deisseroth, L. Ye, and J. T. Vogelstein. 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, J. T. Vogelstein, N. Charon, L. Ye, K. Deisseroth, and M. I. Miller. Deformably registering and annotating whole CLARITY brains to an atlas via masked LDDMM. Optics, Photonics and Digital Technologies for Imaging Applications IV, 2016.

L. Ye, W. E. Allen, K. R. Thompson, Q. Tian, B. Hsueh, C. Ramakrishnan, A. Wang, J. H. Jennings, A. Adhikari, C. H. Halpern, and others. 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, J. Wallace, S. Kim, S. Kalyanasundaram, A. S. Andalman, T. J. Davidson, J. J. Mirzabekov, K. A. Zalocusky, J. Mattis, A. K. Denisin, and others. Structural and molecular interrogation of intact biological systems. Nature, 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