Forge Tools allen_brain_expression

allen_brain_expression read

scidex.forge.allen_brain_expression

Look up Allen Brain Atlas ISH expression energies for a gene across brain regions. Returns top-expressed regions ranked by expression_energy, optionally filtered to a single structure acronym.

HTTP: POST /api/scidex/forge/allen_brain_expression

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.allen_brain_expression``.",
  "properties": {
    "gene_symbol": {
      "description": "Gene symbol to look up in the Allen Brain Atlas. Mouse (``Apoe``, ``Mapt``) and human (``APOE``, ``MAPT``) casing both work — ABA normalises internally.",
      "maxLength": 30,
      "minLength": 1,
      "title": "Gene Symbol",
      "type": "string"
    },
    "region": {
      "anyOf": [
        {
          "maxLength": 20,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Optional ABA structure acronym (``CA1``, ``DG``, ``SN``…) to filter the returned rows. Filter runs client-side; an acronym that does not appear in the top expression rows yields an empty result, not an error.",
      "title": "Region"
    },
    "species": {
      "default": "mouse",
      "description": "Informational species tag. ABA's ISH data is mouse-only at the moment, but the field is preserved for forward compatibility with ABA-Human / Allen Cell Types.",
      "title": "Species",
      "type": "string"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of region rows to return. ABA's hard cap is 200 but the verb caps at 100 to keep one call bounded.",
      "maximum": 100,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol"
  ],
  "title": "AllenBrainExpressionIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "RegionExpression": {
      "description": "One structure's ISH expression summary for the queried gene.",
      "properties": {
        "region_name": {
          "default": "",
          "description": "ABA structure name (e.g. ``Field CA1``).",
          "title": "Region Name",
          "type": "string"
        },
        "region_acronym": {
          "default": "",
          "description": "ABA structure acronym (e.g. ``CA1``).",
          "title": "Region Acronym",
          "type": "string"
        },
        "structure_id": {
          "description": "Numeric ABA structure id.",
          "title": "Structure Id",
          "type": "integer"
        },
        "expression_energy": {
          "default": 0,
          "description": "ABA ``expression_energy`` — sum of expressing pixel intensities divided by structure volume. Comparable within an SDS but not across SDS records.",
          "title": "Expression Energy",
          "type": "number"
        },
        "expression_density": {
          "default": 0,
          "description": "ABA ``expression_density`` — fraction of voxels in the structure with detectable expression (0.0–1.0).",
          "title": "Expression Density",
          "type": "number"
        },
        "sum_expressing_pixels": {
          "default": 0,
          "description": "Raw sum of expressing pixel intensities.",
          "title": "Sum Expressing Pixels",
          "type": "number"
        }
      },
      "required": [
        "structure_id"
      ],
      "title": "RegionExpression",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.allen_brain_expression``.",
  "properties": {
    "gene_symbol": {
      "description": "Echo of the queried gene symbol.",
      "title": "Gene Symbol",
      "type": "string"
    },
    "species": {
      "description": "Echo of the queried species tag.",
      "title": "Species",
      "type": "string"
    },
    "section_data_set_id": {
      "anyOf": [
        {
          "type": "integer"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "ABA SectionDataSet id the expression rows came from. ``None`` when the gene has no ABA coverage.",
      "title": "Section Data Set Id"
    },
    "returned": {
      "description": "Length of ``results``.",
      "title": "Returned",
      "type": "integer"
    },
    "results": {
      "items": {
        "$ref": "#/$defs/RegionExpression"
      },
      "title": "Results",
      "type": "array"
    },
    "took_ms": {
      "description": "Wall-clock time for the upstream calls.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "gene_symbol",
    "species",
    "returned",
    "took_ms"
  ],
  "title": "AllenBrainExpressionOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/allen_brain_expression' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{
  "gene_symbol": ""
}'

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