MIAAIM: multi-modal image alignment and analysis by information manifolds

MIAAIM is a software to align and analyze multi-omics tissue imaging data. The workflow includes high-dimensional image compression and preprocessing, image registration, tissue state modeling, and domain transfer.

MIAAIM was developed by Joshua Hess at the Vaccine and Immunotherapy Center at MGB in the labs of Dr. Ruxandra Sîrbulescu and Dr. Patrick Reeves.

Before using this software, please read the relevant background for each workflow in the pipeline in the Workflows section. For a complete description of the project, check our preprint.

User Guide / Tutorials

• Installation
  • Linux / OS X
  • Windows
  • Installing MIAAIM in Python
• Quick Start
  • TMA013
    • Download Data
    • Image Preprocessing
    • Manual Image Registration
    • Image Registration
    • Image Segmentation
• Folder Structure
  • input
  • hdiprep
  • hdireg
  • docs
• Workflows
  • Image Preparation (HDIprep)
    • YAML Parameter File Input Basics
    • High-Parameter Image Processing
    • Histological Image Processing
    • HDIprep Implementation Guide
  • Image Registration (HDIreg)
    • HDIreg Implementation Guide
  • Tissue State Modelling (PatchMAP)
  • Cross-System/Tissue Information Transfer (i-PatchMAP)
• Parameter Reference
  • HDIprep
  • HDIreg
• Contributing
  • Adding Imaging Modalities
    • Importing New Modalities / Adding File Formats

Quick Start Notebooks

• IMC HDIpreprocessing
  • Set paths to data and get marker information
  • Preprocessing and quality control
  • Create Mask
  • Fill Mask
  • Apply Mask to IMC image
  • Create UMAP embedding of masked IMC image
  • Export Embedding
• MSI Export to HDF5
  • Set paths to csv data with root mean square normalized MSI data
  • Convert to HDF5 and export
• MSI HDIpreprocessing
  • Set paths to data and get marker information
  • Iterate Through Cores and Extract Data
• HE TMA Core Extraction
  • Read Core Labels and Export Individual ROIs
• Training Ilastik
• Ilastik Generate
• HDI Registration
• HDI Segmentation
• Single Cell Quantification

MIAAIM in Python

• Installation
  • Dependencies
  • Usage without Docker / Install with Pip
  • Reproducibility with Pip
  • Docker
  • HDI Utility Functions (hdi-utils)
• Workflow Implementations in Python
  • Image Preparation (HDIprep)
  • Image Registration (HDIreg)
  • Tissue State Modeling (PatchMAP)
  • Cross-System/Tissue Information Transfer (i-PatchMAP)

Background on MIAAIM

• Elastix Basics
  • Registration Parameter Files (Elastix)
  • Applying Transformations (Transformix)

Contributing

• Contributing
  • Adding Imaging Modalities

Contact

• Contact Information

Funding

• Funding

License

• License

Acknowledgements

• Acknowledgements

Indices and tables

• Index

• Module Index

• Search Page