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