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 MHG in the labs of Dr. Ruxandra Sîrbulescu and Dr. Patrick Reeves. It is written in Nextflow with containerized workflows to enable reproducible image data integration across computing architectures.
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.
Note
MIAAIM is under active development! To update your current version, pull the
latest release from GitHub with nextflow pull JoshuaHess12/miaaim.
If you pull a new version, please visit for the latest usage instructions for
new workflows! We will try to make all updated versions backwards compatible
with previous versions. If you are having trouble implementing a
pipeline that you are used to after updating your MIAAIM version,
feel free to contact
us so we can help.
Nextflow User Guide / Tutorials
MIAAIM in Python
Background on MIAAIM
Roadmap
Contributing
FAQs
Contact
Funding
License
Acknowledgements