miaaim

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)
      • Steady-state UMAP compression
      • Histological Image Processing
    • Image Registration (HDIreg)
      • elastix
      • transformix
    • Tissue State Modeling (PatchMAP)
    • Cross-System/Tissue Information Transfer (i-PatchMAP)

Background on MIAAIM

  • Elastix Basics
    • Registration Parameter Files (Elastix)
      • Multi-channel Input
      • Single-channel Input
      • Help the Registration with Manual Landmarks
      • Outputs
    • Applying Transformations (Transformix)

Contributing

  • Contributing
    • Adding Imaging Modalities
      • Importing New Modalities / Adding File Formats

Contact

  • Contact Information

Funding

  • Funding

License

  • License

Acknowledgements

  • Acknowledgements
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© Copyright 2021, Joshua Hess.

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