Datasets:

thanminh01
/

NSCLC-THESIS-WSI-DATASET-EMBEDDING

Error code:   FeaturesError
Exception:    FileNotFoundError
Message:      [Errno 2] No such file or directory: '<datasets.utils.file_utils.FilesIterable object at 0x7f1630034290>'
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 244, in compute_first_rows_from_streaming_response
                  iterable_dataset = iterable_dataset._resolve_features()
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 4408, in _resolve_features
                  features = _infer_features_from_batch(self.with_format(None)._head())
                                                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2679, in _head
                  return next(iter(self.iter(batch_size=n)))
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2861, in iter
                  for key, pa_table in ex_iterable.iter_arrow():
                                       ~~~~~~~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2395, in _iter_arrow
                  yield from self.ex_iterable._iter_arrow()
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 536, in _iter_arrow
                  for key, pa_table in iterator:
                                       ^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 419, in _iter_arrow
                  for key, pa_table in self.generate_tables_fn(**gen_kwags):
                                       ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/xml/xml.py", line 67, in _generate_tables
                  with open(file, encoding=self.config.encoding, errors=self.config.encoding_errors) as f:
                       ~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/streaming.py", line 73, in wrapper
                  return function(*args, download_config=download_config, **kwargs)
                File "/usr/local/lib/python3.14/site-packages/datasets/utils/file_utils.py", line 967, in xopen
                  return open(main_hop, mode, *args, **kwargs)
              FileNotFoundError: [Errno 2] No such file or directory: '<datasets.utils.file_utils.FilesIterable object at 0x7f1630034290>'

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NSCLC-THESIS-WSI-DATASET-EMBEDDING

Public staging mirror for a thesis pipeline (gated acknowledgment before download).
One dataset URL — raw slides under wsi/, precomputed features under embeddings/. Pull only the folder you need.

Repo: thanminh01/NSCLC-THESIS-WSI-DATASET-EMBEDDING

WSI upload of all four cohorts is complete. Integrity checks below passed on 2026-08-14. Embeddings are still empty stubs (thesis Stage 2).

Layout

README.md
manifests/
tooling/               # download scripts + attribution (see tooling/ATTRIBUTION.md)
wsi/
  TCGA-LUAD/          # 541 DX .svs (+ UUID sidecars)
  TCGA-LUSC/          # 512 DX .svs
  CPTAC-LUAD/         # 1137 .svs (flat)
  CPTAC-LSCC/         # 1081 .svs (flat)
clinical/             # per-case companion data (GDC open-access + TCIA), see below
  TCGA-LUAD/{pathology-reports,clinical-supplement,biospecimen-supplement,cases-json}/
  TCGA-LUSC/          # same four subfolders
  CPTAC-LUAD/cases-json/
  CPTAC-LSCC/cases-json/
  CPTAC-tcia-pathology-portal-cohort.csv
  <cohort>-index.csv  # slide -> case -> artifact availability
embeddings/
  README.md
  titan/…             # later — TITAN retrieval embeddings
  gigapath/…          # later — Prov-GigaPath features
  wsi_llava/…         # later — cached descriptions / related

Path	Contents	Approx. size	Status
`wsi/TCGA-LUAD/`	541 diagnostic slides	~415 GB	uploaded, checksum PASS
`wsi/TCGA-LUSC/`	512 diagnostic slides	~409 GB	uploaded, checksum PASS
`wsi/CPTAC-LUAD/`	1137 slides	~429 GB	uploaded, checksum PASS
`wsi/CPTAC-LSCC/`	1081 slides	~415 GB	uploaded, checksum PASS
`clinical/`	pathology reports, clinical + biospecimen supplements, cases JSON, indexes	~600 MB, 5,315 files	uploaded 2026-08-14
`embeddings/*`	precomputed case-bank artifacts	empty stubs	after GPU Stage 2
`manifests/`	GDC manifests, TCGA md5 list, CPTAC `.sums` + verify reports	small	uploaded

Selective download (use `hf`)

REPO=thanminh01/NSCLC-THESIS-WSI-DATASET-EMBEDDING
pip install -U "huggingface_hub[hf_transfer]"
export HF_HUB_ENABLE_HF_TRANSFER=1

# one WSI cohort
hf download "$REPO" --repo-type dataset \
  --include "wsi/TCGA-LUAD/**" \
  --local-dir ./NSCLC-THESIS-WSI-DATASET-EMBEDDING

hf download "$REPO" --repo-type dataset \
  --include "wsi/TCGA-LUSC/**" \
  --local-dir ./NSCLC-THESIS-WSI-DATASET-EMBEDDING

hf download "$REPO" --repo-type dataset \
  --include "wsi/CPTAC-LUAD/**" \
  --local-dir ./NSCLC-THESIS-WSI-DATASET-EMBEDDING

hf download "$REPO" --repo-type dataset \
  --include "wsi/CPTAC-LSCC/**" \
  --local-dir ./NSCLC-THESIS-WSI-DATASET-EMBEDDING

# embeddings only (when populated)
hf download "$REPO" --repo-type dataset \
  --include "embeddings/titan/**" \
  --local-dir ./NSCLC-THESIS-WSI-DATASET-EMBEDDING

# clinical companion data only (small)
hf download "$REPO" --repo-type dataset \
  --include "clinical/**" \
  --local-dir ./NSCLC-THESIS-WSI-DATASET-EMBEDDING

# manifests / card
hf download "$REPO" --repo-type dataset \
  --include "manifests/**" \
  --include "README.md" \
  --local-dir ./NSCLC-THESIS-WSI-DATASET-EMBEDDING

What is uploaded

WSI: full cohort trees as stored after archive download.

TCGA: UUID directories under wsi/TCGA-LUAD/ and wsi/TCGA-LUSC/ (diagnostic DX .svs plus sidecars such as annotations.txt / .parcel). Source manifests: GDC 2023-10-03.
CPTAC: flat .svs under wsi/CPTAC-LUAD/ (package LUAD v12) and wsi/CPTAC-LSCC/ (package LSCC v10), plus package .sums next to the slides and under manifests/.

Embeddings: empty stubs. Filled later from thesis Stage 2 precompute (TITAN, Prov-GigaPath, WSI-LLaVA caches). Derived files still require citing the underlying TCGA/CPTAC sources.

Clinical companion data (`clinical/`)

Everything freely available from GDC and TCIA for the cases behind these slides, fetched 2026-08-14 with GDC-reported MD5 verified on every file (0 failures). Scope = exactly the cases of the 3,271 .svs on this repo.

Cohort	Cases	Cases-API JSON	Pathology report PDFs	Clinical suppl. XML/TSV	Biospecimen suppl.
TCGA-LUAD	478	478/478	479 (every case ≥1)	575	972
TCGA-LUSC	478	478/478	478 (every case ≥1)	546	966
CPTAC-LUAD	244	229/244	none exist on GDC	—	—
CPTAC-LSCC	212	108/212	none exist on GDC	—	—

cases-json/<case>.json — GDC Cases API: primary diagnosis, ICD-O morphology, AJCC stage/TNM, demographics, exposures, samples down to slide-level percent_tumor_nuclei.
pathology-reports/ — TCGA scanned report PDFs (GDC open-access).
clinical-supplement/, biospecimen-supplement/ — per-case XML plus project-wide TSVs (drug, radiation, follow-up, slide tables).
<cohort>-index.csv — one row per slide: case id + artifact counts. Gaps are explicit, not dropped.

Honest limits: GDC hosts no pathology reports or supplements for CPTAC-3 — structured Cases JSON is the maximum there. 15 CPTAC-LUAD and 104 CPTAC-LSCC cases (confirmatory-cohort slides on TCIA) have no GDC record at all; for those, CPTAC-tcia-pathology-portal-cohort.csv (per-slide histology, sex, age, tumor %, GDC/PDC links from the TCIA pathology portal) is the only free metadata. FETCH-SUMMARY.json lists the exact missing case IDs.

Integrity

Verified 2026-08-14. Method: Hugging Face LFS/Xet object sha256 + size compared to (a) GDC manifest sizes for TCGA, (b) streamed local SHA-256 for CPTAC. Zero size or SHA mismatches on .svs.

Cohort	Files	Check	Result	When
`wsi/TCGA-LUAD/`	541 `.svs`	Hub LFS sha256 present; Hub size = GDC manifest size	PASS 541/541	2026-08-14
`wsi/TCGA-LUSC/`	512 `.svs`	same	PASS 512/512	2026-08-14
TCGA `.svs` (prior)	1053	local SHA-256 = Hub LFS oid (Archive copy, since deleted)	PASS 1053/1053	2026-08-09
`wsi/CPTAC-LUAD/`	1137 `.svs`	local SHA-256 = Hub LFS oid; size match	PASS 1137/1137	2026-08-14
`wsi/CPTAC-LSCC/`	1081 `.svs`	local SHA-256 = Hub LFS oid; size match	PASS 1081/1081	2026-08-14

Local TCGA md5 vs GDC (before upload): manifests/md5_compare_report.txt → VERIFY_STATUS=PASS, 1053/1053. Hash list: manifests/downloaded_md5sum_hashes.txt.

CPTAC package checksums: manifests/CPTAC-LUAD_v12.sums, manifests/CPTAC-LSCC.sums. Slide indexes and local verify reports are in manifests/ as well.

TCGA UUID sidecars (annotations.txt, .parcel) are on Hub; small git blobs do not carry an LFS sha256. They are not used as the integrity gate — the .svs objects are.

Intended use

Research / educational computational pathology for this thesis. Not for clinical care.

License / attribution (both sources)

This Hub repo claims no ownership of the underlying archives. Attribute both sides when using any part of this dataset (including embeddings derived from them).

TCGA paths (`wsi/TCGA-*`, and embeddings from them)

Source: TCGA via NCI GDC
Terms: NIH GDS unrestricted-access; no re-identification
Acknowledgment:

The results shown here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga. Data were obtained from the NCI Genomic Data Commons (GDC): https://gdc.cancer.gov/.

CPTAC paths (`wsi/CPTAC-*`, and embeddings from them)

Source: TCIA — CPTAC lung histopathology
License: CC BY 4.0 on Tissue Slide Images for CPTAC-LUAD and CPTAC-LSCC
Policy: TCIA Data Usage Policies and Restrictions
Citations:

National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Lung Adenocarcinoma Collection (CPTAC-LUAD) (Version 13) [dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.PAT12TBS
National Cancer Institute Clinical Proteomic Tumor Analysis Consortium (CPTAC). (2018). The Clinical Proteomic Tumor Analysis Consortium Lung Squamous Cell Carcinoma Collection (CPTAC-LSCC) (Version 15) [dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/K9/TCIA.2018.6EMUB5L2

Download tooling (transparency)

Under tooling/:

Mirror of GeorgeBatch/TCGA-lung-histology-download (scripts + GDC manifests used for this pull). See tooling/ATTRIBUTION.md for license status and citations.
Thesis run notes under tooling/thesis-tcga-download-notes/.

Upstream GitHub lists no SPDX license on that code repo (license: null); we mirror it for provenance only. TCGA/GDC terms still govern all wsi/TCGA-* files.

Limitations

Very large binaries under wsi/; plan disk before a full cohort pull.
Clinical tables not bundled.
Repo is thesis staging, not an official TCGA/TCIA release.

Downloads last month: 2,004

Total file size:

1.73 TB