| --- |
| language: |
| - en |
| license: other |
| license_name: source-data-and-model-terms |
| license_link: https://huggingface.co/datasets/WinstonHu/LoC-Path-Data/blob/main/DATA_TERMS.md |
| tags: |
| - pathology |
| - whole-slide-imaging |
| - visual-question-answering |
| - conch |
| - loc-path |
| configs: |
| - config_name: stage1_reports |
| data_files: |
| - split: train |
| path: annotations/train/stage1_reports.json |
| - config_name: stage2_instructions |
| data_files: |
| - split: train |
| path: annotations/train/stage2_instructions.json |
| --- |
| |
| # LoC-Path Data |
|
|
| > Upload status: complete. All feature files have been checked against the release manifest. |
|
|
| Prepared **WSI-Bench and BCNB** data for LoC-Path training and evaluation: |
| processed annotation JSON, pre-extracted CONCH-v1 features, and coordinates. |
| **Raw whole-slide images, image patches, and original pathology reports are not |
| included.** Model weights are not included. |
|
|
| ## Contents |
|
|
| | Component | Published size | |
| |---|---:| |
| | Stage 1 report-supervision annotations | 9,635 records | |
| | Stage 2 instruction annotations | 175,261 records | |
| | WSI-Bench evaluation annotations (16 task files) | 4,163 records | |
| | BCNB evaluation annotations | 7,274 records | |
| | TCGA slides with NPY feature/coordinate pairs | 9,844 | |
| | BCNB slides with numeric CONCH feature CSVs | 1,058 | |
| | Numeric feature files | 20,746 | |
| | Numeric feature download | 340.62 GB (317.23 GiB) | |
|
|
| The WSI-Bench task partitions are inherited from **WSI-LLaVA/WSI-Bench** through |
| the parent repository's preparation. This release retains those task partitions; |
| it does not create a new partition. Annotation paths are normalized and records |
| without available features are filtered. Published counts therefore describe this |
| prepared snapshot, rather than every upstream annotation version. See |
| [metadata/dataset_summary.json](metadata/dataset_summary.json) for per-file counts |
| and [metadata/excluded_records.json](metadata/excluded_records.json) for omissions. |
|
|
| ## Layout |
|
|
| ```text |
| annotations/ |
| train/stage1_reports.json |
| train/stage2_instructions.json |
| test/wsi_bench/*_test.json |
| test/external/bcnb_choice_test.json |
| features/conch_v1/ |
| <cancer>_224x224_b20_t15/npy_files/ |
| <slide>_features.npy |
| <slide>_coords.npy |
| bcnb_csv/<patient_id>.csv |
| metadata/ |
| dataset_summary.json |
| feature_manifest.json |
| excluded_records.json |
| train_test_overlap.json |
| ``` |
|
|
| Features have shape `[N, 512]`; coordinates have matching shape `[N, 2]` in `(x, y)` |
| order. TCGA NPY arrays retain their existing stored precision without a release-time |
| cast. Model computation follows the training configuration. NPY coordinates use |
| zero-anchored tile-grid indices. BCNB CSVs contain `patch_name` and 512 numeric |
| feature columns; patch names encode coordinates, not image contents. |
|
|
| JSON `image` values are **feature lookup stubs**, not downloadable image paths. |
| For example, `./LUSC/<slide>.h5` resolves to the matching NPY pair in the LoC-Path |
| training loader. BCNB `feature_path` values are relative to `features/conch_v1`. |
| Processed report-generation answers are included as supervision; original source |
| report documents are not distributed. |
|
|
| ## Download and use |
|
|
| ```python |
| from huggingface_hub import snapshot_download |
| |
| snapshot_download( |
| repo_id="WinstonHu/LoC-Path-Data", |
| repo_type="dataset", |
| local_dir="data/LoC-Path-Data", |
| ) |
| ``` |
|
|
| To download only annotations and documentation initially, pass |
| `allow_patterns=["annotations/**", "metadata/**", "README.md", "DATA_TERMS.md"]`. |
| Running the full download again fills in the numeric features. |
|
|
| In the LoC-Path training package: |
|
|
| ```bash |
| export LOCPATH_DATA_ROOT=$PWD/data/LoC-Path-Data |
| export LOCPATH_FEATURE_ROOT="$LOCPATH_DATA_ROOT/features/conch_v1" |
| export LOCPATH_STAGE1_REPORT_JSON="$LOCPATH_DATA_ROOT/annotations/train/stage1_reports.json" |
| export LOCPATH_STAGE1_DATA_PATH="$LOCPATH_STAGE1_REPORT_JSON" |
| export LOCPATH_STAGE2_DATA_PATH="$LOCPATH_DATA_ROOT/annotations/train/stage2_instructions.json" |
| ``` |
|
|
| For WSI-Bench inference, set `DATA_DIR` to |
| `$LOCPATH_DATA_ROOT/annotations/test/wsi_bench`; for BCNB, use |
| `$LOCPATH_DATA_ROOT/annotations/test/external`. Set `FEATURE_ROOT` to |
| `$LOCPATH_FEATURE_ROOT` and pass `--image_feature_suffix .npy` to the inference |
| launcher. BCNB CSV features are selected from each record's relative path. |
| No exclusion CSV is needed for this prepared snapshot. |
|
|
| ## Sources and terms |
|
|
| Annotations are adapted from [WSI-LLaVA/WSI-Bench](https://github.com/XinhengLyu/WSI-LLaVA) |
| and [SlideChat](https://github.com/uni-medical/SlideChat). BCNB numeric features |
| were provided with SlideChat. Features use |
| [CONCH v1](https://huggingface.co/MahmoodLab/CONCH). |
| Read [DATA_TERMS.md](DATA_TERMS.md) for attribution and source-data/model terms. |
| The LoC-Path code license does not relicense these data or the feature extractor. |
|
|
| `metadata/feature_manifest.json` records each numeric file's size, SHA256, feature |
| shape, stored dtype, and annotation memberships. Local source paths and raw assets |
| are excluded from the release. |
|
|
