GreedyFHist

GreedyFHist registers stained histology serial sections to enable precise alignment for integration of spatial omics data such as mass spectrometry imaging (MSI) and spatial transcriptomics (ST).

Key Features:

• Algorithmic Foundation: Based on the principles of the Greedy registration tool and optimized for aligning serial histological sections.
• Registration of stained serial sections: Performs registration of stained serial sections to align tissue morphology across sections.
• Grid projection: Projects spatial omics data onto a grid to enable correspondence between MSI pixels and the spot resolution used in Visium 10x ST.
• Integration with MIIT: Integrates within the Multi-Omics Imaging Integration Toolset (MIIT) to support multi-omics data alignment.
• Validation and performance: Validated on a dataset of 245 pairs of serial sections and reported superior accuracy compared with similar algorithms.

Scientific Applications:

• Multi-omics integration: Enables integration of MSI and ST datasets by providing precise spatial registration between modalities.
• Spatial heterogeneity analysis: Supports analysis of tissue spatial heterogeneity across serial sections for studies of molecular diversity.
• Cancer research and precision medicine: Applied to prostate cancer samples to assess correlations between gene signature activities (e.g., citrate-spermine secretion) and metabolite levels (citrate, spermine, zinc).

Methodology:

Implements Greedy-based registration of stained serial sections and grid projection of spatial omics data.