miaaim

Nextflow User Guide / Tutorials

  • Installation
    • Linux / OS X
    • Windows
    • Installing MIAAIM in Python
  • Quick Start
    • prototype-001
      • Download Data
      • Image Preprocessing
      • Image Registration
  • 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
    • Nextflow
    • HDIprep
    • HDIreg
  • Tutorials
  • Configuration
    • Docker/Singularity Containers
    • Resource Allocation
      • Memory
      • CPU
    • Preset Resource Allocation Options
  • Provenance
  • Contributing
    • Adding Imaging Modalities
      • Importing New Modalities / Adding File Formats

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)
  • Jupyter Notebook Zoo
    • Image Preparation (HDIprep)
    • Image Registration (HDIreg)
    • Tissue State Modelling (PatchMAP)
  • API Guide
    • Image Preparation (HDIprep)
      • hdi_prep
      • utils
    • Image Registration (HDIreg)
      • elastix
      • transformix
      • utils
    • Tissue State Modeling (PatchMAP)
    • Cross-System/Tissue Information Transfer (i-PatchMAP)

Background on MIAAIM

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

Roadmap

  • MIAAIM Roadmap
    • MIAAIM 0.0.1

Contributing

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

FAQs

  • FAQs

Contact

  • Contact Information

Funding

  • Funding

License

  • License

Acknowledgements

  • Acknowledgements
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© Copyright 2021, Joshua Hess.

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