Cortexa research tool·biomedical·cellxgene_census

CELLxGENE Download H5ad

Download original H5AD (HDF5-based AnnData) files from CELLxGENE datasets or get their URIs. Access unprocessed data from individual studies with complete metadata and analysis results. Requires dataset_id from CELLxGENE Discover. Note: Files can be large (GBs). Use for: accessing raw data, reproducibility, offline analysis, custom processing pipelines.

Livelast probed 2026-05-01 01:00Z· 641msCortexa

Status

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

Last probed: 1d ago
Last success: 1d ago
Last latency: 641ms

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"
    },
    "dataset_id": {
      "description": "CELLxGENE dataset identifier (required)",
      "type": "string"
    },
    "operation": {
      "default": "download_h5ad",
      "description": "Operation type",
      "enum": [
        "download_h5ad"
      ],
      "type": "string"
    },
    "output_path": {
      "description": "Local path to save H5AD file (omit to get URI only)",
      "type": "string"
    }
  },
  "required": [
    "operation",
    "dataset_id"
  ],
  "type": "object"
}

Examples (1)

Default CELLxGENE Download H5ad call

public-safeinput

{
  "dataset_id": "",
  "operation": ""
}

Expected response keys: success

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

Identifiers

Catalog ID: tu_CELLxGENE_download_h5ad
Tool name: CELLxGENE_download_h5ad
Added: 2026-05-01 00:58Z
Tags: tooluniverse

CELLxGENE Download H5ad

Livelast probed 2026-05-01 01:00Z· 641msCortexa

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" }, "dataset_id": { "description": "CELLxGENE dataset identifier (required)", "type": "string" }, "operation": { "default": "download_h5ad", "description": "Operation type", "enum": [ "download_h5ad" ], "type": "string" }, "output_path": { "description": "Local path to save H5AD file (omit to get URI only)", "type": "string" } }, "required": [ "operation", "dataset_id" ], "type": "object" }