| --- |
| pretty_name: HistAgent tutorial and Agent Module data |
| license: other |
| task_categories: |
| - image-to-text |
| - text-retrieval |
| language: |
| - en |
| --- |
| |
| # HistAgent tutorial and Agent Module data |
|
|
| This repository contains the public data used by the HistAgent tutorials and |
| the configurable Agent Module. |
|
|
| ## Contents |
|
|
| ```text |
| HistAgent-data/ |
| ├── tutorials/ # tables and images loaded by the notebooks |
| ├── rankridge_tutorial_packs/ |
| │ ├── human__breast/ |
| │ ├── human__kidney/ |
| │ ├── human__stomach/ |
| │ ├── mouse__lung/ |
| │ ├── mouse__spleen/ |
| │ └── rcc__human_kidney/ |
| ├── rankridge_pack_versions.csv |
| ├── rankridge_validation.csv |
| ├── chat/ |
| │ ├── spots.jsonl # 9,150 spatial transcriptomics spot records |
| │ ├── config.example.env # Agent Module data-path configuration |
| │ └── slice_images/ # three RCC tissue images for the slice selector |
| └── manifest.json # byte sizes and SHA-256 checksums |
| ``` |
|
|
| The tutorial files include benchmark summaries, spot examples, clean WSI and |
| ROI images, full-slide HistAgent tile representations and trained ABMIL |
| checkpoints for the three clinical cases shown in the tutorial, the exact |
| patient-level out-of-fold risk tables used for the LIHC and LGG survival |
| panels, and atlas retrieval examples. The STAD examples include all five |
| trained folds used by the displayed score maps; the BRCA example includes the |
| trained OS model used for the displayed local-risk analysis. The |
| RankRidge packs contain sparse reference rank features, reference expression |
| targets, query rank features and fitted coefficients, so the notebooks can run |
| the mapping without downloading the source H5AD collection. |
|
|
| The Agent Module JSONL contains ranked genes, cell-state summaries, pathways and |
| spatial context for each public demo spot. The tissue images use public study |
| accessions as filenames so the server can match them to their slices. |
|
|
| ## Download |
|
|
| ```python |
| from huggingface_hub import snapshot_download |
| |
| root = snapshot_download( |
| "wli13/HistAgent-data", |
| repo_type="dataset", |
| ) |
| ``` |
|
|
| Tutorial notebooks expect: |
|
|
| ```python |
| DATA_DIR = root / "tutorials" |
| RANKRIDGE_DIR = root / "rankridge_tutorial_packs" |
| ``` |
|
|
| The hosted notebooks download only the packs used on the current page. To use |
| a local copy, set `HISTAGENT_TUTORIAL_DATA` and |
| `HISTAGENT_RANKRIDGE_PACKS`. |
|
|
| For the Agent Module: |
|
|
| ```text |
| HISTAGENT_INPUT_JSONL=<root>/chat/spots.jsonl |
| HISTAGENT_ATLAS_SQLITE= |
| HISTAGENT_SLICE_IMAGE_DIRS=<root>/chat/slice_images |
| ``` |
|
|
| The public bundle does not require the optional full-atlas SQLite file. |
| Natural-language retrieval uses the 9,150 rich spot records in `spots.jsonl`. |
|
|
| ## Provenance and use |
|
|
| The bundle contains derived research outputs and examples assembled from the |
| public studies cited by the HistAgent manuscript. Source-study terms continue |
| to apply to the underlying data. |
|
|
