Welcome to MIRACL’s documentation!¶
MIRACL (Multi-modal Image Registration And Connectivity anaLysis) is a general-purpose, open-source pipeline for automated:
- Registration of mice clarity data to the Allen reference atlas
- Segmentation & feature extraction of mice clarity data in 3D (Sparse & nuclear staining)
- Registration of mice multimodal imaging data (MRI & CT, in-vivo & ex-vivo) to Allen reference atlas
- Tract or label specific connectivity analysis based on the Allen connectivity atlas
- Comparison of diffusion tensort imaging (DTI)/tractography, virus tracing using CLARITY & Allen connectivity atlas
- Statistical analysis of CLARITY & Imaging data
- Atlas generation & Label manipulation
Copyright (c) 2019 Maged Goubran, firstname.lastname@example.org
All Rights Reserved.
We provide containers for using the software (Docker and Singularity) as well as local install instructions.