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Nicheverse
Gallery
API reference
Installation
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Viewer
Niche universe
01 Quickstart: train a Nicheverse codebook
02 Transcript context: the segmentation-free molecular field
03 Molecule set: the subcellular transcript point cloud
04 Apply a trained model to new data
05 Annotate codes into cell types and spatial niches
06 Downstream analysis: using the codes and embeddings
Nicheverse on 10x Xenium
Nicheverse on Vizgen MERFISH
Quickstart
Inputs and outputs
Choosing hyperparameters
Annotating codes
MCP server (Claude Code / Codex tools)
GitHub
Gallery
API reference
Installation
Viewer
Niche universe
01 Quickstart: train a Nicheverse codebook
02 Transcript context: the segmentation-free molecular field
03 Molecule set: the subcellular transcript point cloud
04 Apply a trained model to new data
05 Annotate codes into cell types and spatial niches
06 Downstream analysis: using the codes and embeddings
Nicheverse on 10x Xenium
Nicheverse on Vizgen MERFISH
Quickstart
Inputs and outputs
Choosing hyperparameters
Annotating codes
MCP server (Claude Code / Codex tools)
GitHub
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Viewer
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