Jupyter Notebook Zoo

We expect MIAAIM’s workflows to grow as new computational tools become available in the multiplexed imaging community for multi-modal analysis. We have started to compile a “zoo” of jupyter notebooks for each module (with descriptions) so that future users may easily navigate to an application that fits into their workflow. Each workflow in MIAAIM contains its own set of notebooks, stored in the MIAAIM Python repository under the notebooks section.

Image Preparation (HDIprep)

HDIprep Jupyter Notebooks

Workflow	Notebook ID	Data Type (DOI)	Application
HDIprep	001	Prostate MALDI-TOF mass spectrometry imaging (DOI)	Steady-state UMAP compression

Image Registration (HDIreg)

HDIreg Jupyter Notebooks

Workflow	Notebook ID	Data Type (DOI)	Application
HDIreg	001	Prostate MALDI-TOF mass spectrometry imaging and H&E imaging (DOI)	Multi-modal image registration

Tissue State Modelling (PatchMAP)

PatchMAP Jupyter Notebooks

Workflow	Notebook ID	Data Type (DOI)	Application
PatchMAP	001	Scikit-learn digits dataset	Handwritten digit embedding