Q (haiku): is there any imaging data?

▶ read_guide
{
 "uri": "cbioportal://external-resources-guide"
}

◀ result
# External Resources Guide

Use this guide when the user asks about data that may be linked from cBioPortal rather than stored directly in molecular or clinical tables.

## Routing Triggers

Read this guide before answering or refusing questions that mention:

- imaging, radiology, CT, MRI, pathology slides, histology, Minerva, viewer
- external portal, external resource, image data, spatial data
- HTAN studies or study-specific linked viewers

## Core Rule

Do not say cBioPortal has no imaging or external-resource data until you have checked:

- `resource_definition`
- `resource_study`
- `resource_sample`
- `resource_patient`

cBioPortal may store links to external viewers or portals even when it does not store raw images.

## Which Studies Have Imaging Data

For "which studies have imaging / pathology slides / CT" or "how many samples have images", read `cancer_study.resource_sample_counts` — per-study sample counts keyed by resource display name, the same numbers as the portal's "Data type" filter. One query, no joins:

```sql
SELECT
    cancer_study_identifier,
    name,
    resource_sample_counts['Slide Microscopy'] AS slide_microscopy_samples
FROM cancer_study
WHERE resource_sample_counts['Slide Microscopy'] > 0
ORDER BY slide_microscopy_samples DESC;
```

List the resource names that exist with `SELECT DISTINCT arrayJoin(mapKeys(resource_sample_counts)) FROM cancer_study` (e.g. `'Slide Microscopy'`, `'Computed Tomography'`, `'Magnetic Resonance'`, `'H&E Slide'`, `'MxIF Image'`).

The map counts sample- and patient-level resources only. For study-level links (`resource_study`) and for the URLs themselves, use the queries below.

## Discovery Query

Start with table and column validation, then use this pattern:

```sql
SELECT
    rd.resource_id,
    rd.display_name,
    rd.description,
    rd.resource_type,
    rs.cancer_study_identifier,
    rs.url
FROM resource_study rs
JOIN resource_definition rd
    ON rs.resource_id = rd.resource_id
WHERE lower(rd.display_name) LIKE '%minerva%'
   OR lower(rd.description) LIKE '%minerva%'
   OR lower(rd.display_name) LIKE '%image%'
   OR lower(rd.description) LIKE '%image%'
   OR lower(rd.display_name) LIKE '%pathology%'
   OR lower(rd.description) LIKE '%pathology%'
   OR lower(rd.display_name) LIKE '%histology%'
   OR lower(rd.description) LIKE '%histology%'
ORDER BY rs.cancer_study_identifier, rd.display_name
LIMIT 100;
```

If no study-level rows appear, check sample- and patient-level resource links:

```sql
SELECT
    rd.resource_id,
    rd.display_name,
    rd.description,
    rs.cancer_study_identifier,
    rs.sample_unique_id,
    rs.url
FROM resource_sample rs
JOIN resource_definition rd
    ON rs.resource_id = rd.resource_id
WHERE lower(rd.display_name) LIKE '%minerva%'
   OR lower(rd.description) LIKE '%minerva%'
   OR lower(rd.display_name) LIKE '%image%'
   OR lower(rd.description) LIKE '%image%'
   OR lower(rd.display_name) LIKE '%pathology%'
   OR lower(rd.description) LIKE '%pathology%' … (981 more chars)

▶ clickhouse_list_table_columns
{
 "table": "resource_definition"
}

▶ clickhouse_list_table_columns
{
 "table": "resource_study"
}

◀ result
{"columns":[{"name":"resource_id","type":"String"},{"name":"display_name","type":"String"},{"name":"description","type":"Nullable(String)"},{"name":"resource_type","type":"String"},{"name":"open_by_default","type":"Nullable(Int32)"},{"name":"priority","type":"Int64"},{"name":"cancer_study_id","type":"Int64"},{"name":"custom_metadata","type":"Nullable(String)"}]}

▶ clickhouse_list_table_columns
{
 "table": "cancer_study"
}

◀ result
{"columns":[{"name":"internal_id","type":"Int64"},{"name":"resource_id","type":"String"},{"name":"url","type":"String"}]}

◀ result
{"columns":[{"name":"cancer_study_id","type":"Int64","comment":"Internal numeric ID. Prefer cancer_study_identifier for queries as it is more readable and stable."},{"name":"cancer_study_identifier","type":"Nullable(String)","comment":"Stable string identifier for the study (e.g., \"msk_chord_2024\", \"brca_tcga\"). Use this for filtering, not cancer_study_id."},{"name":"type_of_cancer_id","type":"String"},{"name":"name","type":"String","comment":"Full descriptive name of the study (e.g., \"MSK-CHORD (MSK, Nature 2024)\")."},{"name":"description","type":"String"},{"name":"public","type":"Int32"},{"name":"pmid","type":"Nullable(String)"},{"name":"citation","type":"Nullable(String)"},{"name":"groups","type":"Nullable(String)"},{"name":"status","type":"Nullable(Int64)"},{"name":"import_date","type":"Nullable(DateTime64(6))"},{"name":"reference_genome_id","type":"Nullable(Int64)"},{"name":"sample_count","type":"UInt32","comment":"Samples in the study (members of <study>_all), as shown in the portal study list. Precomputed daily at LLM-prep time."},{"name":"mutation_sample_count","type":"UInt32","comment":"Samples profiled for mutations (<study>_sequenced) — portal \"Data type\" filter: \"Mutations\". 0 = no mutation data."},{"name":"cna_sample_count","type":"UInt32","comment":"Samples profiled for copy-number alterations (<study>_cna) — \"CNA\". 0 = no CNA data."},{"name":"structural_variant_sample_count","type":"UInt32","comment":"Distinct samples with at least one structural variant (fusions etc.). 0 = none."},{"name":"rna_seq_sample_count","type":"UInt32","comment":"Samples with RNA-Seq expression (<study>_rna_seq_v2_mrna) — \"RNA-Seq\"."},{"name":"mrna_microarray_sample_count","type":"UInt32","comment":"Samples with microarray mRNA expression (<study>_mrna) — \"RNA (microarray)\"."},{"name":"mirna_sample_count","type":"UInt32","comment":"Samples with microRNA expression (<study>_microrna) — \"miRNA\"."},{"name":"rppa_sample_count","type":"UInt32","comment":"Samples with RPPA protein levels (<study>_rppa) — \"RPPA\"."},{"name":"mass_spectrometry_sample_count","type":"UInt32","comment":"Samples with mass-spectrometry protein quantification (<study>_protein_quantification) — \"Protein Mass-Spectrometry\"."},{"name":"treatment_patient_count","type":"UInt32","comment":"PATIENTS (not samples) with treatment clinical events — \"Treatment\". 0 = no treatment data."},{"name":"resource_sample_counts","type":"Map(String, UInt32)","comment":"Samples with each linked resource, keyed by display name: imaging and pathology such as 'Slide Microscopy', 'Computed Tomography', 'Magnetic Resonance', 'H&E Slide', 'MxIF Image'. Query with mapKeys(resource_sample_counts) or resource_sample_counts['Slide Microscopy'] > 0."},{"name":"mrna_expression_sample_count","type":"UInt32","comment":"Samples in any mRNA expression profile (RNA-Seq, microarray, TPM, z-scores; from sample_profile). Use this for \"does the study have expression data\" — rna_seq_sample_count and mrna_m … (136 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT DISTINCT arrayJoin(mapKeys(resource_sample_counts)) AS resource_type
FROM cancer_study
WHERE resource_sample_counts != {}
ORDER BY resource_type
",
 "max_rows": 50
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 62\n Code: 62. DB::Exception: Syntax error: failed at position 143 (}) (line 3, col 34): }\nORDER BY resource_type) LIMIT 51\n FORMAT Native. Expected substitution name (identifier). (SYNTAX_ERROR) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_run_select_query
{
 "query": "
SELECT
    cancer_study_identifier,
    name,
    mapKeys(resource_sample_counts) AS resource_types,
    resource_sample_counts
FROM cancer_study
WHERE resource_sample_counts != {}
ORDER BY cancer_study_identifier
LIMIT 50
",
 "max_rows": 50
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 62\n Code: 62. DB::Exception: Syntax error: failed at position 195 (}) (line 7, col 34): }\nORDER BY cancer_study_identifier\nLIMIT 50) LIMIT 51\n FORMAT Native. Expected substitution name (identifier). (SYNTAX_ERROR) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_run_select_query
{
 "query": "
SELECT
    rd.resource_id,
    rd.display_name,
    rd.description,
    rd.resource_type,
    COUNT(DISTINCT rs.internal_id) AS study_count
FROM resource_definition rd
LEFT JOIN resource_study rs ON rd.resource_id = rs.resource_id
GROUP BY rd.resource_id, rd.display_name, rd.description, rd.resource_type
ORDER BY study_count DESC, rd.display_name
LIMIT 50
",
 "max_rows": 50
}

◀ result
{"rows":[{"resource_id":"CHROMOSCOPE","display_name":"Chromoscope","description":"Link to Chromoscope","resource_type":"SAMPLE","study_count":1},{"resource_id":"IDC_OHIF_CR","display_name":"Computed Radiography","description":"Computed Radiography","resource_type":"PATIENT","study_count":1},{"resource_id":"IDC_OHIF_CT","display_name":"Computed Tomography","description":"Computed Tomography","resource_type":"PATIENT","study_count":1},{"resource_id":"CYCIF","display_name":"CyCIF","description":"CyCIF","resource_type":"SAMPLE","study_count":1},{"resource_id":"IDC_OHIF_DX","display_name":"Digital Radiography","description":"Digital Radiography","resource_type":"PATIENT","study_count":1},{"resource_id":"FIGURES","display_name":"Figures","description":"Figures from https://www.biorxiv.org/content/10.1101/2020.12.03.408500v1/","resource_type":"PATIENT","study_count":1},{"resource_id":"HE","display_name":"H&E Slide","description":"H&E Slide","resource_type":"SAMPLE","study_count":1},{"resource_id":"IDC_OHIF_MR","display_name":"Magnetic Resonance","description":"Magnetic Resonance","resource_type":"PATIENT","study_count":1},{"resource_id":"IDC_OHIF_MG","display_name":"Mammography","description":"Mammography","resource_type":"PATIENT","study_count":1},{"resource_id":"MXIF","display_name":"MxIF Image","description":"MxIF Images","resource_type":"SAMPLE","study_count":1},{"resource_id":"MXIF","display_name":"MxIF Image","description":"MxIF Images","resource_type":"PATIENT","study_count":1},{"resource_id":"IDC_OHIF_NM","display_name":"Nuclear Medicine","description":"Nuclear Medicine","resource_type":"PATIENT","study_count":1},{"resource_id":"IDC_OHIF_PT","display_name":"Positron Emission Tomography","description":"Positron Emission Tomography","resource_type":"PATIENT","study_count":1},{"resource_id":"IDC_SLIM","display_name":"Slide Microscopy","description":"Slide Microscopy","resource_type":"PATIENT","study_count":1}]}

▶ clickhouse_run_select_query
{
 "query": "
SELECT
    cancer_study_identifier,
    name,
    sample_count
FROM cancer_study
WHERE cancer_study_identifier IN (
    SELECT DISTINCT cancer_study_identifier
    FROM cancer_study
    WHERE mapLength(resource_sample_counts) > 0
)
ORDER BY cancer_study_identifier
",
 "max_rows": 100
}

◀ result
{"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 46\n Code: 46. DB::Exception: Function with name `mapLength` does not exist. In scope (SELECT DISTINCT cancer_study_identifier FROM cancer_study WHERE mapLength(resource_sample_counts) > 0). Maybe you meant: ['length']. (UNKNOWN_FUNCTION) (version 26.4.1.2359 (official build))\n"}

▶ clickhouse_run_select_query
{
 "query": "
SELECT
    cancer_study_identifier,
    name,
    sample_count
FROM cancer_study
WHERE length(resource_sample_counts) > 0
ORDER BY cancer_study_identifier
",
 "max_rows": 100
}

◀ result
{"rows":[{"cancer_study_identifier":"acc_tcga_pan_can_atlas_2018","name":"Adrenocortical Carcinoma (TCGA, PanCancer Atlas)","sample_count":92},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018","name":"Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)","sample_count":411},{"cancer_study_identifier":"brca_aurora_2023","name":"Metastatic Breast Cancer (AURORA US Network, Nat Cancer 2023)","sample_count":155},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","sample_count":1084},{"cancer_study_identifier":"cesc_tcga_pan_can_atlas_2018","name":"Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas)","sample_count":297},{"cancer_study_identifier":"chol_tcga_pan_can_atlas_2018","name":"Cholangiocarcinoma (TCGA, PanCancer Atlas)","sample_count":36},{"cancer_study_identifier":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)","sample_count":594},{"cancer_study_identifier":"crc_hta11_htan_2021","name":"Pre-cancer Colorectal Polyps (HTAN Vanderbilt, Cell 2021)","sample_count":61},{"cancer_study_identifier":"crc_hta8_htan_2024","name":"Colorectal Cancer (HTAN MSK, Nature 2025)","sample_count":83},{"cancer_study_identifier":"crc_orion_2024","name":"Colorectal Adenocarcinoma (DFCI/Orion, BioRxiv 2024)","sample_count":74},{"cancer_study_identifier":"difg_glass","name":"Diffuse Glioma (GLASS Consortium)","sample_count":693},{"cancer_study_identifier":"dlbc_tcga_pan_can_atlas_2018","name":"Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas)","sample_count":48},{"cancer_study_identifier":"esca_tcga_pan_can_atlas_2018","name":"Esophageal Adenocarcinoma (TCGA, PanCancer Atlas)","sample_count":182},{"cancer_study_identifier":"gbm_tcga_pan_can_atlas_2018","name":"Glioblastoma Multiforme (TCGA, PanCancer Atlas)","sample_count":592},{"cancer_study_identifier":"hnsc_tcga_pan_can_atlas_2018","name":"Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas)","sample_count":523},{"cancer_study_identifier":"kich_tcga_pan_can_atlas_2018","name":"Kidney Chromophobe (TCGA, PanCancer Atlas)","sample_count":65},{"cancer_study_identifier":"kirc_tcga_pan_can_atlas_2018","name":"Kidney Renal Clear Cell Carcinoma (TCGA, PanCancer Atlas)","sample_count":512},{"cancer_study_identifier":"kirp_tcga_pan_can_atlas_2018","name":"Kidney Renal Papillary Cell Carcinoma (TCGA, PanCancer Atlas)","sample_count":283},{"cancer_study_identifier":"lgg_tcga_pan_can_atlas_2018","name":"Brain Lower Grade Glioma (TCGA, PanCancer Atlas)","sample_count":514},{"cancer_study_identifier":"lihc_tcga_pan_can_atlas_2018","name":"Liver Hepatocellular Carcinoma (TCGA, PanCancer Atlas)","sample_count":372},{"cancer_study_identifier":"luad_tcga_pan_can_atlas_2018","name":"Lung Adenocarcinoma (TCGA, PanCancer Atlas)","sample_count":566},{"cancer_study_identifier":"lusc_tcga_pan_can_atlas_2018","name":"Lung Squamous Cell Carcinoma (TCGA, PanCancer Atlas)","sample_count":487},{"cancer_study_i … (2120 more chars)

▶ clickhouse_run_select_query
{
 "query": "
SELECT
    cancer_study_identifier,
    name,
    arrayJoin(mapKeys(resource_sample_counts)) AS resource_type,
    resource_sample_counts[arrayJoin(mapKeys(resource_sample_counts))] AS sample_count
FROM cancer_study
WHERE length(resource_sample_counts) > 0
ORDER BY cancer_study_identifier, resource_type
",
 "max_rows": 150
}

◀ result
{"rows":[{"cancer_study_identifier":"acc_tcga_pan_can_atlas_2018","name":"Adrenocortical Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Slide Microscopy","sample_count":91},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018","name":"Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Computed Radiography","sample_count":7},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018","name":"Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Computed Tomography","sample_count":107},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018","name":"Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Digital Radiography","sample_count":7},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018","name":"Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Magnetic Resonance","sample_count":20},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018","name":"Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Positron Emission Tomography","sample_count":7},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018","name":"Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Slide Microscopy","sample_count":411},{"cancer_study_identifier":"brca_aurora_2023","name":"Metastatic Breast Cancer (AURORA US Network, Nat Cancer 2023)","resource_type":"H&E Slide","sample_count":142},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Magnetic Resonance","sample_count":136},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Mammography","sample_count":5},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Slide Microscopy","sample_count":1084},{"cancer_study_identifier":"cesc_tcga_pan_can_atlas_2018","name":"Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Magnetic Resonance","sample_count":53},{"cancer_study_identifier":"cesc_tcga_pan_can_atlas_2018","name":"Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas)","resource_type":"Slide Microscopy","sample_count":297},{"cancer_study_identifier":"chol_tcga_pan_can_atlas_2018","name":"Cholangiocarcinoma (TCGA, PanCancer Atlas)","resource_type":"Slide Microscopy","sample_count":36},{"cancer_study_identifier":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)","resource_type":"Computed Tomography","sample_count":21},{"cancer_study_identifier":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)","resource_type":"Slide Microscopy","sample_count":594},{"cancer_study_identifier":"crc_hta11_htan_2021","name":"Pre-cancer Colorectal Polyps (HTAN Vanderbilt, Cell 2021)","resource_type":"H&E Slide","sample_count":26},{"cancer_study_identifier":"crc_hta11_ … (10959 more chars)

═ answer (success)
Yes, cBioPortal has extensive imaging data! Here's what's available:

## **Imaging & Pathology Resources**

cBioPortal links to **external imaging viewers and pathology data** across **37 studies**. These are not stored as raw images in the database, but rather as links to specialized viewers.

### **Types of Imaging Data Available**

1. **Slide Microscopy** (most common) — 14,845 samples across 36 studies
   - H&E staining, histopathology from pathology labs
   - Available in all TCGA PanCancer Atlas studies

2. **Medical Imaging** — via the Imaging Data Commons (IDC) OHIF viewer
   - **Computed Tomography (CT)** — 825 samples across 12 studies
   - **Magnetic Resonance Imaging (MRI)** — 349 samples across 7 studies
   - **Positron Emission Tomography (PET)** — 64 samples across 6 studies
   - **Computed/Digital Radiography** — 16 samples
   - **Mammography** — 5 samples
   - **Nuclear Medicine** — 4 samples

3. **High-Resolution Imaging**
   - **MxIF (Multiplex immunoFluorescence)** — 131 samples (colorectal, ovarian studies)
   - **CyCIF (Cyclic immunoFluorescence)** — 567 samples (ovarian cancer, Gray Foundation study)
   - **H&E Slides** — 215 samples (breast, colorectal, glioma studies)

### **Key Studies with Imaging**

- **TCGA PanCancer Atlas** (33 cancer types) — all have slide microscopy; many have CT/MRI
- **Colorectal Cancer (HTAN MSK, 2025)** — 58 MxIF samples
- **Ovarian Cancer (Gray Foundation, 2024)** — 567 CyCIF samples  
- **Metastatic Breast Cancer (AURORA, 2023)** — 142 H&E slides
- **Kidney Renal Clear Cell Carcinoma (TCGA)** — 221 CT, 60 MRI samples

### **How to Access**

When you navigate to a **patient or sample** in cBioPortal, imaging links appear in the **Resources** section. Medical imaging (CT, MRI, PET) links to the **Imaging Data Commons (IDC) OHIF Viewer**, enabling pan-and-zoom, 3D reconstruction, and multi-modality viewing.

Would you like me to show you how to access imaging data for a specific cancer type or patient?