๐๏ธ Mastering Spatial Analysis of Multiplex Imaging Data with SCIMAP
This series is designed to equip researchers, data scientists, and enthusiasts with the knowledge and tools necessary to unlock the full potential of spatial analysis techniques. Whether you're new to the field or looking to deepen your understanding, these tutorials will guide you through the intricacies of analyzing complex imaging data, enabling you to uncover the spatial relationships and patterns that lie within.
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Set up
๐ค Install Scimap
๐ฅ Download demo data
๐ Prepare demo data for analysis
Cell Phenotyping
๐คน๐ผโโ๏ธ Phenotype cells by unsupervised clustering
๐ฝ Phenotype cells using a hierarchical probabilistic model
๐ Add Regions of Interest (ROIs) for exploration
๐คฉ Explore the composition of defined cell types between samples and ROIs
Spatial Analysis
๐ Calculate and visualize distances between cell types
๐ค Cell-cell interaction/ co-occurrence analysis
โ๏ธ Compare proximity scores between samples
๐ญ Search for spatial patterns
Cellular Neighbourhoods
๐ณ Compute neighborhoods using cell-type or cluster information (includes LDA method)
๐ Compute neighborhoods using expression data
Export and Helper Functions
โฌ๏ธ Export analysis results to .csv
๐ฉโ๐จ Animate with scimap
๐ Merge objects, Classify cells etc..
Videos
๐ฅ Video tutorials