Explorer¶
Interactive maps for navigating the spatial omics landscape. Switch between the Pipeline Map (analysis workflow) and the Technology Compatibility Map (platform-tool matrix).
Click a node to highlight its connections. Category nodes show representative tools as smaller child nodes. Drag nodes to rearrange.
Click a technology or tool node to see its connections. Edges indicate documented compatibility.
About These Maps¶
Pipeline Map¶
Shows the data flow through a typical spatial omics analysis pipeline. Nodes are colored by analysis step, and directed edges indicate which steps feed into each other. Small tool nodes branch off each category to show representative methods.
Key patterns visible in the map:
- Segmentation is the central hub -- most downstream analyses (SVG detection, spatial domains, deconvolution, CCC, DE) depend on cell-level data from segmentation
- Multiple paths to niches -- niche identification can be reached via spatial domains or CCC, reflecting different analytical philosophies
- Convergence at visualization -- all analysis steps ultimately feed into visualization and interpretation frameworks like Squidpy and SpatialData
Technology Compatibility Map¶
Shows which analysis tools have been validated with which technology platforms. Edges indicate documented compatibility in the tool's paper or documentation.
Key patterns:
- Visium has the broadest tool support -- as the most widely adopted platform, nearly every tool has been tested on Visium data
- Imaging-based platforms (Xenium, MERFISH, CosMx) share segmentation tools -- Cellpose, Baysor, and StarDist work across all single-molecule resolution platforms
- Spot-based tools (BayesSpace, RCTD, Cell2location) cluster around Visium -- these methods were designed for the multi-cell spot resolution
- Framework tools (Squidpy, SpatialData) are technology-agnostic -- they connect to nearly every platform