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 and feature extraction of mice CLARITY data in 3D (Sparse and 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 and Allen Connectivity Atlas

  6. Statistical analysis of CLARITY and imaging data

  7. Atlas generation and Label manipulation

We recommend using MIRACL with the Docker or Singularity containers we provide but it can also be installed locally. See our installation instructions for more information.

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