MIRACL (Multi-modal Image Registration And Connectivity anaLysis) is a general-purpose, open-source pipeline for automated:
1) Registration of mice clarity data to the Allen reference atlas
2) Segmentation & feature extraction of mice clarity data in 3D (Sparse & nuclear staining)
3) Registration of mice multimodal imaging data (MRI & CT, in-vivo & ex-vivo) to Allen reference atlas
4) Tract or label specific connectivity analysis based on the Allen connectivity atlas
5) Comparison of diffusion tensort imaging (DTI)/tractography, virus tracing using CLARITY &
Allen connectivity atlas
6) Statistical analysis of CLARITY & Imaging data
7) Atlas generation & Label manipulation
Copyright (c) 2022 Maged Goubran, [email protected]
All Rights Reserved.
We provide containers for using the software (Docker and Singularity) as well as
local install instructions. For more details, see our docs.
Note that the base image for the docker container can be found in docker and
the container mgoubran/miracl is built on top of that.