Q (sonnet): 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_run_select_query { "query": "SELECT DISTINCT arrayJoin(mapKeys(resource_sample_counts)) AS resource_name FROM cancer_study" } ◀ result {"rows":[{"resource_name":"H&E Slide"},{"resource_name":"MxIF Image"},{"resource_name":"CyCIF"},{"resource_name":"Slide Microscopy"},{"resource_name":"Magnetic Resonance"},{"resource_name":"Positron Emission Tomography"},{"resource_name":"Computed Tomography"},{"resource_name":"Nuclear Medicine"},{"resource_name":"Computed Radiography"},{"resource_name":"Mammography"},{"resource_name":"Digital Radiography"}]} ▶ clickhouse_run_select_query { "query": " 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 ORDER BY rs.cancer_study_identifier, rd.display_name LIMIT 100 " } ◀ result {"error_message":"Query execution failed: HTTPDriver for https://dl96orhu96.us-east-1.aws.clickhouse.cloud:8443 received ClickHouse error code 47\n Code: 47. DB::Exception: Identifier 'rs.cancer_study_identifier' cannot be resolved from table with name rs. In scope SELECT rd.resource_id, rd.display_name, rd.description, rd.resource_type, rs.cancer_study_identifier, rs.url FROM resource_study AS rs INNER JOIN resource_definition AS rd ON rs.resource_id = rd.resource_id ORDER BY rs.cancer_study_identifier ASC, rd.display_name ASC LIMIT 100. (UNKNOWN_IDENTIFIER) (version 26.4.1.2359 (official build))\n"} ▶ clickhouse_list_table_columns { "table": "resource_study" } ◀ result {"columns":[{"name":"internal_id","type":"Int64"},{"name":"resource_id","type":"String"},{"name":"url","type":"String"}]} ▶ clickhouse_run_select_query { "query": " SELECT cancer_study_identifier, name, resource_sample_counts['Slide Microscopy'] AS slide_microscopy, resource_sample_counts['H&E Slide'] AS he_slide, resource_sample_counts['MxIF Image'] AS mxif, resource_sample_counts['CyCIF'] AS cycif, resource_sample_counts['Magnetic Resonance'] AS mri, resource_sample_counts['Positron Emission Tomography'] AS pet, resource_sample_counts['Computed Tomography'] AS ct, resource_sample_counts['Nuclear Medicine'] AS nuc_med, resource_sample_counts['Computed Radiography'] AS comp_rad, resource_sample_counts['Mammography'] AS mammo, resource_sample_counts['Digital Radiography'] AS dig_rad FROM cancer_study WHERE resource_sample_counts['Slide Microscopy'] > 0 OR resource_sample_counts['H&E Slide'] > 0 OR resource_sample_counts['MxIF Image'] > 0 OR resource_sample_counts['CyCIF'] > 0 OR resource_sample_counts['Magnetic Resonance'] > 0 OR resource_sample_counts['Positron Emission Tomography'] > 0 OR resource_sample_counts['Computed Tomography'] > 0 OR resource_sample_counts['Nuclear Medicine'] > 0 OR resource_sample_counts['Computed Radiography'] > 0 OR resource_sample_counts['Mammography'] > 0 OR resource_sample_counts['Digital Radiography'] > 0 ORDER BY cancer_study_identifier " } ◀ result {"rows":[{"cancer_study_identifier":"acc_tcga_pan_can_atlas_2018","name":"Adrenocortical Carcinoma (TCGA, PanCancer Atlas)","slide_microscopy":91,"he_slide":0,"mxif":0,"cycif":0,"mri":0,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"blca_tcga_pan_can_atlas_2018","name":"Bladder Urothelial Carcinoma (TCGA, PanCancer Atlas)","slide_microscopy":411,"he_slide":0,"mxif":0,"cycif":0,"mri":20,"pet":7,"ct":107,"nuc_med":0,"comp_rad":7,"mammo":0,"dig_rad":7},{"cancer_study_identifier":"brca_aurora_2023","name":"Metastatic Breast Cancer (AURORA US Network, Nat Cancer 2023)","slide_microscopy":0,"he_slide":142,"mxif":0,"cycif":0,"mri":0,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"brca_tcga_pan_can_atlas_2018","name":"Breast Invasive Carcinoma (TCGA, PanCancer Atlas)","slide_microscopy":1084,"he_slide":0,"mxif":0,"cycif":0,"mri":136,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":5,"dig_rad":0},{"cancer_study_identifier":"cesc_tcga_pan_can_atlas_2018","name":"Cervical Squamous Cell Carcinoma (TCGA, PanCancer Atlas)","slide_microscopy":297,"he_slide":0,"mxif":0,"cycif":0,"mri":53,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"chol_tcga_pan_can_atlas_2018","name":"Cholangiocarcinoma (TCGA, PanCancer Atlas)","slide_microscopy":36,"he_slide":0,"mxif":0,"cycif":0,"mri":0,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"coadread_tcga_pan_can_atlas_2018","name":"Colorectal Adenocarcinoma (TCGA, PanCancer Atlas)","slide_microscopy":594,"he_slide":0,"mxif":0,"cycif":0,"mri":0,"pet":0,"ct":21,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"crc_hta11_htan_2021","name":"Pre-cancer Colorectal Polyps (HTAN Vanderbilt, Cell 2021)","slide_microscopy":0,"he_slide":26,"mxif":25,"cycif":0,"mri":0,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"crc_hta8_htan_2024","name":"Colorectal Cancer (HTAN MSK, Nature 2025)","slide_microscopy":0,"he_slide":0,"mxif":58,"cycif":0,"mri":0,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"crc_orion_2024","name":"Colorectal Adenocarcinoma (DFCI/Orion, BioRxiv 2024)","slide_microscopy":0,"he_slide":0,"mxif":40,"cycif":0,"mri":0,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"difg_glass","name":"Diffuse Glioma (GLASS Consortium)","slide_microscopy":0,"he_slide":10,"mxif":0,"cycif":0,"mri":0,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"dlbc_tcga_pan_can_atlas_2018","name":"Diffuse Large B-Cell Lymphoma (TCGA, PanCancer Atlas)","slide_microscopy":48,"he_slide":0,"mxif":0,"cycif":0,"mri":0,"pet":0,"ct":0,"nuc_med":0,"comp_rad":0,"mammo":0,"dig_rad":0},{"cancer_study_identifier":"esca_tcga_pan_can_atlas_2018","name":"Esophageal Adenocarcinoma (TCGA, PanCancer Atlas)","slide_micr … (6173 more chars) ═ answer (success) Yes — cBioPortal links out to imaging and pathology data for a substantial number of studies, though the underlying pixel data lives in external viewers/repositories (e.g. TCIA, Minerva-style slide viewers), not inside cBioPortal itself. Highlights across 37 studies with linked imaging resources: **Slide microscopy / digital pathology** (whole-slide histology images) — present in nearly all TCGA PanCancer Atlas studies, e.g.: - [Breast Invasive Carcinoma (TCGA, PanCancer Atlas)](https://www.cbioportal.org/study/summary?id=brca_tcga_pan_can_atlas_2018) — 1,084 samples - [Ovarian Serous Cystadenocarcinoma (TCGA)](https://www.cbioportal.org/study/summary?id=ov_tcga_pan_can_atlas_2018) — 575 samples - [Glioblastoma Multiforme (TCGA)](https://www.cbioportal.org/study/summary?id=gbm_tcga_pan_can_atlas_2018) — 592 samples **Radiology (CT, MRI, PET, mammography, nuclear medicine)** — smaller subsets, notably: - [Kidney Renal Clear Cell Carcinoma (TCGA)](https://www.cbioportal.org/study/summary?id=kirc_tcga_pan_can_atlas_2018) — 221 CT, 60 MRI - [Bladder Urothelial Carcinoma (TCGA)](https://www.cbioportal.org/study/summary?id=blca_tcga_pan_can_atlas_2018) — 107 CT, 20 MRI, 7 PET - [Ovarian Serous Cystadenocarcinoma (TCGA)](https://www.cbioportal.org/study/summary?id=ov_tcga_pan_can_atlas_2018) — 140 CT **Multiplexed/spatial imaging (H&E, MxIF, CyCIF)** — mostly newer HTAN/spatial-biology cohorts: - [Ovarian Cancer, Gray Foundation (Cancer Discov 2024)](https://www.cbioportal.org/study/summary?id=ovary_geomx_gray_foundation_2024) — 567 CyCIF samples - [Ovarian Cancer – MSK SPECTRUM](https://www.cbioportal.org/study/summary?id=msk_spectrum_tme_2022) — 37 H&E + 8 MxIF - [Colorectal Cancer, HTAN MSK (Nature 2025)](https://www.cbioportal.org/study/summary?id=crc_hta8_htan_2024) — 58 MxIF - [Metastatic Breast Cancer, AURORA (Nat Cancer 2023)](https://www.cbioportal.org/study/summary?id=brca_aurora_2023) — 142 H&E These counts reflect samples with a linked imaging resource, not raw images stored in cBioPortal's own database — clicking through opens an external viewer (e.g. slide viewer or TCIA). Do you want me to open the study view for a specific one of these (or a specific cancer type) so you can browse the linked images directly?