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cafferychen777

ChatSpatial

by cafferychen777
OverviewSchemaRelated ServersScoreDiscussions
Python
Hybrid

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault

No arguments

Capabilities

Features and capabilities supported by this server

CapabilityDetails
tools
{
  "listChanged": false
}
prompts
{
  "listChanged": false
}
resources
{
  "subscribe": false,
  "listChanged": false
}
experimental
{}

Tools

Functions exposed to the LLM to take actions

NameDescription
load_data

Load spatial transcriptomics data with comprehensive metadata profile.

Args:
    data_path: Path to data file or directory
    data_type: 'visium', 'xenium', 'slide_seq', 'merfish', 'seqfish', or 'generic'
    name: Optional dataset name

Returns:
    SpatialDataset with cell/gene counts and metadata profiles
preprocess_data

Preprocess spatial transcriptomics data (QC, normalization, HVGs, PCA, clustering, spatial neighbors).

Args:
    data_id: Dataset ID
    params: Preprocessing parameters (all have sensible defaults)
compute_embeddings

Compute dimensionality reduction (PCA, UMAP), clustering, and neighbor graphs.

Args:
    data_id: Dataset ID
    params: Embedding parameters (PCA, UMAP, clustering, etc.)
visualize_data

Visualize spatial transcriptomics data. Set plot_type and subtype in params; see VisualizationParameters schema for all options.

Args:
    data_id: Dataset ID
    params: Visualization parameters (plot_type, subtype, genes, output_format, dpi, etc.)
annotate_cell_types

Annotate cell types in spatial transcriptomics data.

Args:
    data_id: Dataset ID
    params: Annotation parameters (method, reference_data_id, cell_type_key, etc.)

Note: Reference methods (tangram, scanvi) require reference_data_id to be preprocessed first.
analyze_spatial_statistics

Analyze spatial statistics and autocorrelation patterns.

Args:
    data_id: Dataset ID
    params: Analysis parameters (analysis_type, cluster_key, genes). See SpatialStatisticsParameters for all types.
find_markers

Find differentially expressed genes between groups.

Args:
    data_id: Dataset ID
    params: Required - group_key and optional method, group1/group2, n_top_genes, etc.
compare_conditions

Compare experimental conditions using pseudobulk differential expression (DESeq2).

Args:
    data_id: Dataset ID
    params: Required - condition_key, condition1, condition2, sample_key, etc.
analyze_cnv

Analyze copy number variations (CNVs) in spatial transcriptomics data.

Args:
    data_id: Dataset identifier
    params: Required - reference_key, reference_categories, and optional method/thresholds.
analyze_velocity_data

Analyze RNA velocity to understand cellular dynamics. Requires 'spliced' and 'unspliced' layers.

Args:
    data_id: Dataset ID
    params: Velocity parameters (method, scvelo_mode, etc.)
analyze_trajectory_data

Infer cellular trajectories and pseudotime ordering.

Args:
    data_id: Dataset ID
    params: Trajectory parameters (method, root_cell, spatial_weight, etc.)
integrate_samples

Integrate multiple spatial transcriptomics samples into a unified dataset.

Args:
    data_ids: List of dataset IDs to integrate
    params: Integration parameters (method, batch_key, n_pcs, etc.)
deconvolve_data

Deconvolve spatial spots to estimate cell type proportions.

Args:
    data_id: Dataset ID
    params: Required - method, cell_type_key, reference_data_id. See DeconvolutionParameters for all methods and options.
identify_spatial_domains

Identify spatial domains and tissue architecture.

Args:
    data_id: Dataset ID
    params: Spatial domain parameters (method, n_domains, resolution, etc.)
analyze_cell_communication

Analyze cell-cell communication and ligand-receptor interaction patterns.

Args:
    data_id: Dataset ID
    params: Required - species, cell_type_key, and method. For mouse with liana, set liana_resource='mouseconsensus'.
analyze_enrichment

Perform gene set enrichment analysis.

Args:
    data_id: Dataset ID
    params: Required - species must be specified. See EnrichmentParameters for methods and gene_set_database options.
find_spatial_genes

Identify spatially variable genes.

Args:
    data_id: Dataset ID
    params: Spatial variable gene parameters (method, n_top_genes, etc.)
register_spatial_data

Register/align spatial transcriptomics data across sections

Args:
    source_id: Source dataset ID
    target_id: Target dataset ID to align to
    params: Registration parameters (method, alignment settings, etc.)

Returns:
    Registration result with method, dataset IDs, spot counts, and registered spatial key
export_data

Export dataset to disk for external script access.

Args:
    data_id: Dataset ID to export
    path: Custom path (default: ~/.chatspatial/active/{data_id}.h5ad)

Returns:
    Absolute path where data was exported
reload_data

Reload dataset from disk after external script modifications.

Args:
    data_id: Dataset ID to reload (must exist in MCP memory)
    path: Custom path (default: ~/.chatspatial/active/{data_id}.h5ad)

Returns:
    Summary of reloaded dataset

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

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