Cortexa research tool·biomedical·cellxgene_census

CELLxGENE Get Embeddings

Access pre-calculated cell embeddings (scVI, Geneformer) from CELLxGENE Census. Returns available embedding names or specific embedding data. Embeddings enable rapid visualization and analysis without recomputation. Use for: UMAP/t-SNE visualization, cell similarity analysis, transfer learning.

Livelast probed 2026-04-30 23:07Z· 98msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 98ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "census_version": {
      "default": "stable",
      "description": "Census version to query. 'stable' (recommended, Long-Term Support release), 'latest' (newest data, may change), or specific date 'YYYY-MM-DD' (for reproducibility). Default 'stable' is best for production analyses.",
      "type": "string"
    },
    "embedding_name": {
      "description": "Name of specific embedding to retrieve (omit to list available embeddings)",
      "type": "string"
    },
    "operation": {
      "default": "get_embeddings",
      "description": "Operation type",
      "enum": [
        "get_embeddings"
      ],
      "type": "string"
    },
    "organism": {
      "default": "Homo sapiens",
      "description": "Organism name",
      "enum": [
        "Homo sapiens",
        "Mus musculus"
      ],
      "type": "string"
    }
  },
  "required": [
    "operation"
  ],
  "type": "object"
}

Examples (1)

Default CELLxGENE Get Embeddings call

public-safeinput

{
  "operation": ""
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_CELLxGENE_get_embeddings
Tool name: CELLxGENE_get_embeddings
Added: 2026-04-30 22:47Z
Tags: tooluniverse

CELLxGENE Get Embeddings

Livelast probed 2026-04-30 23:07Z· 98msCortexa

Schema

JSON Schema the agent (or your API call) must match.

{ "properties": { "census_version": { "default": "stable", "description": "Census version to query. 'stable' (recommended, Long-Term Support release), 'latest' (newest data, may change), or specific date 'YYYY-MM-DD' (for reproducibility). Default 'stable' is best for production analyses.", "type": "string" }, "embedding_name": { "description": "Name of specific embedding to retrieve (omit to list available embeddings)", "type": "string" }, "operation": { "default": "get_embeddings", "description": "Operation type", "enum": [ "get_embeddings" ], "type": "string" }, "organism": { "default": "Homo sapiens", "description": "Organism name", "enum": [ "Homo sapiens", "Mus musculus" ], "type": "string" } }, "required": [ "operation" ], "type": "object" }