Claritomes

About

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.

Data

Tools

ndreg is a Python package that performs non-linear affine and deformable image registration.

ndreg

Publications

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

People on project

Vikram Chandrashekhar
Ailey Crow
Joshua Vogelstein
Karl Deisseroth

Funding

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