{"id":"idc-pdxnet","title":"PDXNet","short_title":"pdxnet","aliases":["pdxnet"],"summary":"A pan-cancer repository of 5,420 DICOM Slide Microscopy instances from 919 patient-derived xenograft (PDX) and paired parental tumor H&E whole slide images (870 mouse PDX, 49 human progenitor) curated from the NCI PDXNet Consortium. Images have associated genomic, transcriptomic, and clinical metadata, as well as pathologic assessments and, in some cases, detailed pathologic annotations. The original TIFF and SVS images were converted to DICOM SM format. Please see the PDXNet Zenodo page to learn more about the images and to obtain any supporting metadata for this collection.","one_liner":null,"identifiers":[{"scheme":"idc_collection_id","value":"pdxnet","url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=pdxnet","is_primary":true,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/pdxnet","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"tcia_collection","value":"PDXNet","url":"https://www.cancerimagingarchive.net/collections/","is_primary":false,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/pdxnet","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"scheme":"zenodo","value":"10.5281/zenodo.16967600","url":null,"is_primary":false,"evidence":[{"method":"fulltext","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/pdxnet","source_label":"IDC collection description","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":"The original TIFF and SVS images were converted to DICOM SM format. Please see the PDXNet Zenodo page to learn more about the images and to obtain any supporting metadata for this collection.","locator":"accession extracted from description prose","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Cross-repository link recovered from prose; verify before relying on it."}]}],"repository":{"name":"NCI Imaging Data Commons","short_name":"IDC","url":"https://portal.imaging.datacommons.cancer.gov","is_nci_crdc_node":true,"is_nih_repository":true},"additional_repositories":[],"program_name":"NCI Imaging Data Commons / The Cancer Imaging Archive","program_url":"https://imaging.datacommons.cancer.gov/","nci_program":"IDC","generating_institutions":[],"data_generation_funding_role":"unknown","version":null,"release_date":null,"last_upstream_update":null,"retrieved_at":"2026-09-18T02:44:36.389375Z","landing_page_url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=pdxnet","cancer_types":[{"label":"Acinar Cell Carcinoma","ontology":null,"code":null,"url":null},{"label":"Adrenal Cortical Carcinoma","ontology":null,"code":null,"url":null},{"label":"Carcinosarcoma","ontology":null,"code":null,"url":null},{"label":"Chondrosarcoma","ontology":null,"code":null,"url":null},{"label":"Colon Adenocarcinoma","ontology":null,"code":null,"url":null},{"label":"Ewing Sarcoma","ontology":null,"code":null,"url":null},{"label":"Gastrointestinal Stromal Tumor","ontology":null,"code":null,"url":null},{"label":"Head and Neck Squamous Cell Carcinoma","ontology":null,"code":null,"url":null},{"label":"Invasive Breast Carcinoma","ontology":null,"code":null,"url":null},{"label":"Invasive Breast Carcinoma of No Special Type","ontology":null,"code":null,"url":null},{"label":"Leiomyosarcoma","ontology":null,"code":null,"url":null},{"label":"Lung Adenocarcinoma","ontology":null,"code":null,"url":null},{"label":"Lung Squamous Cell Carcinoma","ontology":null,"code":null,"url":null},{"label":"Malignant Peripheral Nerve Sheath Tumor","ontology":null,"code":null,"url":null},{"label":"Melanoma","ontology":null,"code":null,"url":null},{"label":"Merkel Cell Carcinoma","ontology":null,"code":null,"url":null},{"label":"Mesothelial Neoplasm","ontology":null,"code":null,"url":null},{"label":"Mucoepidermoid Carcinoma","ontology":null,"code":null,"url":null},{"label":"Myxofibrosarcoma","ontology":null,"code":null,"url":null},{"label":"Neuroendocrine Carcinoma","ontology":null,"code":null,"url":null},{"label":"Non-Small Cell Carcinoma","ontology":null,"code":null,"url":null},{"label":"Osteosarcoma","ontology":null,"code":null,"url":null},{"label":"Pancreatic Adenocarcinoma","ontology":null,"code":null,"url":null},{"label":"Renal Cell Carcinoma","ontology":null,"code":null,"url":null},{"label":"Not Otherwise Specified","ontology":null,"code":null,"url":null},{"label":"Rhabdomyosarcoma","ontology":null,"code":null,"url":null},{"label":"Spindle Cell Sarcoma","ontology":null,"code":null,"url":null},{"label":"Synovial Sarcoma","ontology":null,"code":null,"url":null},{"label":"Transitional Cell Carcinoma","ontology":null,"code":null,"url":null},{"label":"Urothelial Carcinoma","ontology":null,"code":null,"url":null}],"primary_sites":["adrenal gland","bladder organ","bone element","breast","colon","gallbladder","genitourinary system","larynx","lip","oral cavity","lung","ovary","pancreas","peripheral nervous system","prostate gland","rectum","skin of body","small intestine","thyroid gland","uterine cervix","uterus","stomach","vagina"],"subject":{"scope":"pan_cancer","tissues":[],"evidence":[{"method":"derived","source_url":null,"source_label":"cds.subjects","retrieved_at":null,"snippet":null,"locator":"cancer_types: Acinar Cell Carcinoma, Adrenal Cortical Carcinoma, Carcinosarcoma, Chondrosarcoma, Colon Adenocarcinoma, Ewing Sarcoma, Gastrointestinal Stromal Tumor, Head and Neck Squamous Cell Carcinoma, Invasive Breast Carcinoma, Invasive Breast Carcinoma of No Special Type, Leiomyosarcoma, Lung Adenocarcinoma, Lung Squamous Cell Carcinoma, Malignant Peripheral Nerve Sheath Tumor, Melanoma, Merkel Cell Carcinoma, Mesothelial Neoplasm, Mucoepidermoid Carcinoma, Myxofibrosarcoma, Neuroendocrine Carcinoma, Non-Small Cell Carcinoma, Osteosarcoma, Pancreatic Adenocarcinoma, Renal Cell Carcinoma, Not Otherwise Specified, Rhabdomyosarcoma, Spindle Cell Sarcoma, Synovial Sarcoma, Transitional Cell Carcinoma, Urothelial Carcinoma; primary_sites: adrenal gland, bladder organ, bone element, breast, colon, gallbladder, genitourinary system, larynx, lip, oral cavity, lung, ovary, pancreas, peripheral nervous system, prostate gland, rectum, skin of body, small intestine, thyroid gland, uterine cervix, uterus, stomach, vagina","confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Four or more repository-stated tissues make this pan-cancer."}]},"is_pediatric":null,"model_systems":[],"cohort":{"n_cases":919,"n_samples":null,"n_aliquots":null,"n_files":null,"total_bytes":null,"n_tumor_cases":null,"n_normal_cases":null,"has_matched_normal":null,"demographics":{"sex":{},"race":{},"ethnicity":{},"age_at_diagnosis_years":{},"vital_status":{},"country_or_region":{},"evidence":[]},"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/pdxnet","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"assays":[{"modality":"radiology","label":"DICOM medical imaging","platform":null,"n_cases":919,"n_samples":null,"n_files":null,"data_levels":["DICOM series"],"access_tier":"open","evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/pdxnet","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"clinical","label":"Clinical (accompanying data, per IDC supporting_data)","platform":null,"n_cases":null,"n_samples":null,"n_files":null,"data_levels":[],"access_tier":null,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/pdxnet","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":"field: supporting_data","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]},{"modality":"wgs","label":"Genomics (accompanying data, per IDC supporting_data)","platform":null,"n_cases":null,"n_samples":null,"n_files":null,"data_levels":[],"access_tier":null,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/pdxnet","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":"field: supporting_data","confidence":"medium","reviewer":null,"reviewed_at":null,"note":null}]}],"clinical_variables":[],"longitudinal":{"has_followup":null,"has_survival_endpoint":null,"survival_endpoints":[],"median_followup_months":null,"max_followup_months":null,"n_cases_with_followup":null,"has_serial_samples":null,"timepoints":[],"n_cases_with_serial":null,"has_treatment_response":null,"response_criteria":[],"evidence":[]},"access":{"tier":"open","open_components":[],"controlled_components":[],"mechanism":"Public DICOM download from the IDC portal, its API, or the idc-index Python package; no account required for public collections.","dua_url":null,"data_access_committee":null,"typical_turnaround":null,"embargo_until":null,"login_required":false,"citation_requirement":"Cite the collection DOI and the IDC/TCIA data-citation guidance.","license":"Per-collection license, typically CC BY 3.0/4.0 or CC BY-NC","publication_policy_url":"https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/","evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/collections/pdxnet","source_label":"IDC v3 API /collections","retrieved_at":"2026-09-18T02:44:36.389375Z","snippet":null,"locator":null,"confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]},"useful_for":[],"limitations":[{"kind":"missing_data","statement":"IDC serves no clinical table for this collection, so nothing about outcome, stage, treatment or demographics can be read from the repository. Any such variable would have to come from the originating trial or publication. The collection's own supporting_data field nevertheless lists clinical data, so the two disagree.","severity":"blocking","affected_analyses":["survival","treatment response","stage-adjusted modelling","analysis by race or ethnicity"],"mitigation":null,"evidence":[{"method":"api","source_url":"https://api.imaging.datacommons.cancer.gov/v3/clinical/tables","source_label":"IDC v3 API /clinical/tables","retrieved_at":"2026-09-19T03:20:46.830869Z","snippet":null,"locator":"collection_id=pdxnet: no clinical table is served","confidence":"high","reviewer":null,"reviewed_at":null,"note":null}]}],"inappropriate_uses":[],"primary_publications":[],"reuse":[],"reuse_metrics":{"n_candidates_screened":0,"n_by_tier":{},"n_by_tier_raw":{},"accession_precision":null,"n_citations_to_primary_publication":null,"citation_to_reuse_ratio":null,"has_citable_accession":false,"n_verified_reuse":null,"n_reuse_examined":0,"n_independent_reuse":0,"n_nci_funded_reuse":0,"first_reuse_year":null,"latest_reuse_year":null,"years_since_release":null,"expected_reuse":null,"reuse_gap_index":null,"reuse_gap_percentile":null,"search_strategy_id":"epmc-index-v3","searched_at":"2026-09-20T18:07:30.926466Z","no_reuse_identified":false,"evidence":[{"method":"derived","source_url":null,"source_label":"reuse index","retrieved_at":"2026-09-20T18:07:30.926466Z","snippet":null,"locator":null,"confidence":"low","reviewer":null,"reviewed_at":null,"note":"This dataset has no accession specific enough to search for in the literature, so citation-based reuse cannot be measured. Absence of a count here is not evidence of absence of reuse."}]},"underexplored":{"is_underexplored":false,"basis":["Not assessed: this dataset has no accession specific enough for citation-based reuse tracing, so a shortfall cannot be measured."],"index_value":null,"percentile":null,"comparator_set":"rgi-huber-v2","evidence":[]},"grants":[],"access_steps":[{"order":1,"action":"Open the collection in the IDC portal","detail":"Browse the series before downloading; imaging collections can be very large.","url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=pdxnet","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://portal.imaging.datacommons.cancer.gov/explore/?collection_id=pdxnet","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.429038Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":2,"action":"Read the collection's own licence","detail":"Per-collection license, typically CC BY 3.0/4.0 or CC BY-NC. IDC licences differ by collection.","url":"https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/","requires":[],"est_time":"5 minutes","cli_snippet":null,"audience":"human","evidence":[{"method":"derived","source_url":"https://www.cancerimagingarchive.net/data-usage-policies-and-restrictions/","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.429040Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":3,"action":"Download with idc-index","detail":"The package resolves the collection to its buckets and pulls selected data.","url":"https://github.com/ImagingDataCommons/idc-index","requires":[],"est_time":"hours for a full collection","cli_snippet":"pip install idc-index\npython - <<'PY'\nfrom idc_index import IDCClient\nIDCClient().download_from_selection(collection_id=\"pdxnet\", downloadDir=\".\")\nPY","audience":"human","evidence":[{"method":"derived","source_url":"https://github.com/ImagingDataCommons/idc-index","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.429042Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]},{"order":4,"action":"List the series before pulling pixels","detail":"List modality and size first so an agent can choose what to fetch.","url":"https://learn.canceridc.dev/","requires":[],"est_time":null,"cli_snippet":"python - <<'PY'\nfrom idc_index import IDCClient\ni = IDCClient().index\ns = i[i[\"collection_id\"] == \"pdxnet\"]\nprint(len(s), \"series\", s[\"PatientID\"].nunique(), \"patients\",\n      round(s[\"series_size_MB\"].sum() / 1024, 1), \"GB\")\nprint(s[\"Modality\"].value_counts().to_dict())\nPY","audience":"agent","evidence":[{"method":"derived","source_url":"https://learn.canceridc.dev/","source_label":"IDC access documentation","retrieved_at":"2026-09-21T12:30:59.429044Z","snippet":null,"locator":null,"confidence":"medium","reviewer":null,"reviewed_at":null,"note":"Generated by applying the repository's documented access policy to this dataset's identifiers. It is not a reviewer's account of this dataset."}]}],"analysis_examples":[],"agent_package":{"json_url":"/data/datasets/idc-pdxnet.json","jsonld_url":"/data/jsonld/idc-pdxnet.jsonld","croissant_url":"/data/croissant/idc-pdxnet.json","instructions_url":"/data/agent/idc-pdxnet.md","bundle_url":null,"mcp_resource_uri":null},"related_dataset_ids":[],"related_underexplored_ids":[],"review":{"status":"machine_only","reviewer":null,"reviewer_affiliation":null,"reviewed_at":null,"sections_reviewed":[],"open_questions":[],"notes":null},"verification":{"last_verified_at":null,"link_checks":[],"n_links_ok":0,"n_links_broken":0,"upstream_version_seen":null,"upstream_version_changed":false,"upstream_counts_seen":{},"upstream_drift":{},"notes":[]},"is_showcase":false,"completeness_score":16.1,"tags":["idc","imaging","imaging-genomics"],"search_text":null}