Welcome to MIRACL’s documentation!

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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) 2019 Maged Goubran, maged.goubran@utoronto.ca

All Rights Reserved.


We provide containers for using the software (Docker and Singularity) as well as local install instructions.