Table 1 Modifiable parameter decisions across modules

From: A multimodal framework to identify molecular mechanisms driving patient group-associated morphology through the integration of spatial transcriptomics and whole slide imaging

 

Module 1- Preprocessing and Style Transfer

Module 2- Predictive modeling and clustering

Module 3- Mapping

Module 4- Molecular Analyses

Parameters

• Tile size

• Color normalization method

• % tile overlap

• Foundation model (RetCCL, Virchow, Uni, etc)

• MIL model (attention-MIL, TransMIL, CLAM, etc)

• % threshold for top attention tiles

• Clustering type (leiden, louvain, etc)

• k for KNN

No defaults in our framework - users can dive deeper into each molecular analysis tool for customization (C-side, SpatialDM)

Back to article page