ChatSpatial

deconvolve_data

Destructive

Estimate cell type proportions from spatial transcriptomics spots by matching them against single-cell reference data with multiple methods.

Instructions

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.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`params`	Yes
`data_id`	Yes

Output Schema

TableJSON Schema

Name	Required	Description
`method`	Yes
`data_id`	Yes
`n_spots`	No
`warnings`	No	Non-fatal conditions that may affect result interpretation.
`cell_types`	Yes
`genes_used`	No
`n_cell_types`	Yes
`proportions_key`	Yes
`dominant_type_key`	Yes

Schema Changelog

Changes observed during successful MCP inspections. Dates show when Glama detected each change.

Changed25 schema fields changedv1.3.2Aug 10, 2026
- addedInput schema / $defs / DeconvolutionParameters / additionalProperties
```
Added value: +false
```
- removedInput schema / $defs / DeconvolutionParameters / properties / cell2location_early_stopping_threshold / exclusiveMinimum
```
Removed value: -0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / cell2location_early_stopping_threshold / minimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / cell2location_gene_filter_cell_count_cutoff / minimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / cell2location_gene_filter_cell_percentage_cutoff2 / maximum
```
Added value: +1
```
- addedInput schema / $defs / DeconvolutionParameters / properties / cell2location_gene_filter_cell_percentage_cutoff2 / minimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / cell2location_gene_filter_nonz_mean_cutoff / minimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / destvi_dropout_rate / exclusiveMaximum
```
Added value: +1
```
- addedInput schema / $defs / DeconvolutionParameters / properties / destvi_dropout_rate / minimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / destvi_learning_rate / exclusiveMinimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / destvi_n_hidden / exclusiveMinimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / destvi_n_latent / exclusiveMinimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / destvi_n_layers / exclusiveMinimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / rctd_backend
```
Added value: +{
+  "default": "r",
+  "description": "RCTD implementation. 'r' preserves the spacexr backend; 'python' uses rctd-py.",
+  "enum": [
+    "r",
+    "python"
+  ],
+  "title": "Rctd Backend",
+  "type": "string"
+}
```
- addedInput schema / $defs / DeconvolutionParameters / properties / rctd_batch_size
```
Added value: +{
+  "anyOf": [
+    {
+      "exclusiveMinimum": 0,
+      "type": "integer"
+    },
+    {
+      "const": "auto",
+      "type": "string"
+    }
+  ],
+  "default": "auto",
+  "description": "Spot batch size for the rctd-py backend, or 'auto'.",
+  "title": "Rctd Batch Size"
+}
```
- addedInput schema / $defs / DeconvolutionParameters / properties / rctd_device
```
Added value: +{
+  "default": "auto",
+  "description": "Compute device for the rctd-py backend. Ignored by the R backend.",
+  "enum": [
+    "auto",
+    "cpu",
+    "cuda"
+  ],
+  "title": "Rctd Device",
+  "type": "string"
+}
```
- addedInput schema / $defs / DeconvolutionParameters / properties / rctd_dtype
```
Added value: +{
+  "default": "float64",
+  "description": "Numerical precision for the rctd-py backend.",
+  "enum": [
+    "float64",
+    "float32"
+  ],
+  "title": "Rctd Dtype",
+  "type": "string"
+}
```
- addedInput schema / $defs / DeconvolutionParameters / properties / rctd_sigma_override
```
Added value: +{
+  "anyOf": [
+    {
+      "exclusiveMinimum": 0,
+      "type": "integer"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Optional fixed sigma for rctd-py. None estimates sigma from the data.",
+  "title": "Rctd Sigma Override"
+}
```
- addedInput schema / $defs / DeconvolutionParameters / properties / stereoscope_batch_size / exclusiveMinimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / stereoscope_learning_rate / exclusiveMinimum
```
Added value: +0
```
- addedInput schema / $defs / DeconvolutionParameters / properties / stereoscope_n_epochs / exclusiveMinimum
```
Added value: +0
```
- addedInput schema / additionalProperties
```
Added value: +false
```
- addedOutput schema / additionalProperties
```
Added value: +false
```
- removedOutput schema / properties / statistics
```
Removed value: -{
-  "additionalProperties": true,
-  "title": "Statistics",
-  "type": "object"
-}
```
- addedOutput schema / properties / warnings
```
Added value: +{
+  "description": "Non-fatal conditions that may affect result interpretation.",
+  "items": {
+    "type": "string"
+  },
+  "title": "Warnings",
+  "type": "array"
+}
```
Changed3 schema fields changedv1.2.10May 21, 2026
- changedInput schema / $defs / DeconvolutionParameters / properties / spotlight_n_top_genes / default
```
Previous value: -2000New value: +50
```
- changedInput schema / $defs / DeconvolutionParameters / properties / spotlight_n_top_genes / description
```
Previous value: -"Number of HVGs for deconvolution. SPOTlight only."New value: +"Marker genes per cell type for SPOTlight deconvolution."
```
- changedInput schema / $defs / DeconvolutionParameters / properties / spotlight_n_top_genes / maximum
```
Previous value: -5000New value: +500
```
First observedv1.2.7May 11, 2026

TDQS

A3.5/5.0

Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare destructiveHint=true, readOnlyHint=false, and idempotentHint=false, so the safety profile is externally known. However, the description adds no behavioral transparency beyond the basic operation—it does not mention overwriting previous results, requiring pre-loaded reference data, compute time, or other runtime effects.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is compact and well-structured: one sentence of purpose, one sentence of parameter pointers. It is front-loaded with the core purpose and avoids unnecessary elaboration, making every sentence earn its place.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's high complexity (8 deconvolution methods and many method-specific parameters), the description is minimal but not fatally incomplete because the schema and annotations carry substantial detail. Still, it lacks guidance on method selection, data prerequisites, or expected outcomes, leaving the agent to rely heavily on structured fields.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

The description compensates for the 0% schema coverage by explicitly naming the effectively required trio: method, cell_type_key, and reference_data_id. This goes beyond the schema, which only marks cell_type_key as required. However, it does not explain the meaning of each parameter or how to choose methods, deferring entirely to DeconvolutionParameters.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description starts with the specific action verb 'Deconvolve' on 'spatial spots' and clearly states the outcome: 'estimate cell type proportions.' This uniquely distinguishes the tool from siblings like analyze_spatial_statistics or identify_spatial_domains, which have different analytical goals.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description implies usage when cell type proportion estimates are needed, but it provides no explicit when-to-use/when-not-to-use guidance or alternatives among sibling tools. The only additional guidance is a list of required parameters, which is more about invocation than usage context.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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