miaaim

User Guide / Tutorials

Installation
Quick Start
- TMA013
Folder Structure
- input
- hdiprep
- hdireg
- docs
Workflows
Parameter Reference
- HDIprep
- HDIreg
Contributing
- Adding Imaging Modalities
  - Importing New Modalities / Adding File Formats

Quick Start Notebooks

IMC HDIpreprocessing
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
Workflow Implementations in Python

Background on MIAAIM

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

Contributing

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

Contact

Contact Information

Funding

Funding

License

License

Acknowledgements

Acknowledgements

miaaim

Index
Edit on GitHub

Index

© Copyright 2021, Joshua Hess.

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